NM_000914.5(OPRM1):c.13G>A (p.Ala5Thr) AND not specified

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jun 29, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV004237635.1

Allele description [Variation Report for NM_000914.5(OPRM1):c.13G>A (p.Ala5Thr)]

NM_000914.5(OPRM1):c.13G>A (p.Ala5Thr)

Gene:

OPRM1:opioid receptor mu 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q25.2

Genomic location:

Preferred name:

NM_000914.5(OPRM1):c.13G>A (p.Ala5Thr)

HGVS:

NC_000006.12:g.154039557G>A
NG_021208.2:g.34057G>A
NG_109509.1:g.158G>A
NM_000914.5:c.13G>AMANE SELECT
NM_001008503.3:c.13G>A
NM_001008504.4:c.13G>A
NM_001008505.2:c.13G>A
NM_001145279.4:c.292G>A
NM_001145280.4:c.-11+28539G>A
NM_001145281.3:c.47+28998G>A
NM_001145282.2:c.13G>A
NM_001145283.2:c.13G>A
NM_001145284.3:c.13G>A
NM_001145285.3:c.13G>A
NM_001145286.3:c.13G>A
NM_001285522.1:c.13G>A
NM_001285523.3:c.13G>A
NM_001285524.1:c.292G>A
NP_000905.3:p.Ala5Thr
NP_001008503.2:p.Ala5Thr
NP_001008504.2:p.Ala5Thr
NP_001008505.2:p.Ala5Thr
NP_001138751.1:p.Ala98Thr
NP_001138754.1:p.Ala5Thr
NP_001138755.1:p.Ala5Thr
NP_001138756.1:p.Ala5Thr
NP_001138757.1:p.Ala5Thr
NP_001138758.1:p.Ala5Thr
NP_001272451.1:p.Ala5Thr
NP_001272452.1:p.Ala5Thr
NP_001272453.1:p.Ala98Thr
LRG_1007t1:c.13G>A
LRG_1007t2:c.13G>A
LRG_1007:g.34057G>A
LRG_1007p1:p.Ala5Thr
LRG_1007p2:p.Ala5Thr
NC_000006.11:g.154360692G>A
NM_000914.3:c.13G>A
NR_104348.1:n.147G>A
NR_104349.1:n.147G>A
NR_104350.1:n.147G>A
NR_104351.1:n.147G>A

Protein change:

A5T

Molecular consequence:

NM_001145280.4:c.-11+28539G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001145281.3:c.47+28998G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000914.5:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001008503.3:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001008504.4:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001008505.2:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001145279.4:c.292G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001145282.2:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001145283.2:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001145284.3:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001145285.3:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001145286.3:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001285522.1:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001285523.3:c.13G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001285524.1:c.292G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_104348.1:n.147G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104349.1:n.147G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104350.1:n.147G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104351.1:n.147G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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Krameria secundiflora isolate 23 clone 10 internal transcribed spacer 1, partial...
Krameria secundiflora isolate 23 clone 10 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|30171992|gb|AY261120.1|

Nucleotide
NADH dehydrogenase subunit 5 (mitochondrion) [Propithecus verreauxi]
NADH dehydrogenase subunit 5 (mitochondrion) [Propithecus verreauxi]
gi|944542650|ref|YP_009176583.1|

Protein
Propithecus verreauxi voucher LAH8.31 mitochondrion, complete genome
Propithecus verreauxi voucher LAH8.31 mitochondrion, complete genome
gi|2267399554|gb|OM650058.1|

Nucleotide
Propithecus edwardsi voucher FAN6.8 mitochondrion, partial genome
Propithecus edwardsi voucher FAN6.8 mitochondrion, partial genome
gi|2267398546|gb|OM649986.1|

Nucleotide
Propithecus edwardsi voucher RANO344 mitochondrion, partial genome
Propithecus edwardsi voucher RANO344 mitochondrion, partial genome
gi|2267398518|gb|OM649984.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003753844	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jun 29, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003753844

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jun 29, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV003753844.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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