NM_015404.4(WHRN):c.668G>A (p.Arg223His) AND not provided

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 29, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000839182.10

Allele description [Variation Report for NM_015404.4(WHRN):c.668G>A (p.Arg223His)]

NM_015404.4(WHRN):c.668G>A (p.Arg223His)

Gene:

WHRN:whirlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q32

Genomic location:

Preferred name:

NM_015404.4(WHRN):c.668G>A (p.Arg223His)

HGVS:

NC_000009.12:g.114478722C>T
NG_016700.1:g.31735G>A
NM_001083885.3:c.-482G>A
NM_001173425.2:c.668G>A
NM_015404.4:c.668G>AMANE SELECT
NP_001166896.1:p.Arg223His
NP_056219.3:p.Arg223His
LRG_1094t1:c.668G>A
LRG_1094:g.31735G>A
LRG_1094p1:p.Arg223His
NC_000009.11:g.117241002C>T
NM_015404.2:c.668G>A
NM_015404.3:c.668G>A
c.668G>A

Protein change:

R223H

Links:

dbSNP: rs146273185

NCBI 1000 Genomes Browser:

rs146273185

Molecular consequence:

NM_001083885.3:c.-482G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001173425.2:c.668G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015404.4:c.668G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Nucleotide-diphospho-sugar transferase family protein [Arabidopsis thaliana]
Nucleotide-diphospho-sugar transferase family protein [Arabidopsis thaliana]
gi|1063696536|ref|NP_001322084.1|

Protein
Homo sapiens methionine adenosyltransferase 2 non-catalytic beta subunit (MAT2B)...
Homo sapiens methionine adenosyltransferase 2 non-catalytic beta subunit (MAT2B), transcript variant 2, mRNA
gi|422010900|ref|NM_182796.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000981066	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Jun 18, 2018)	germline	clinical testing	Citation Link,
SCV001032870	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000981066

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(Jun 18, 2018)

germline

clinical testing

Citation Link,

SCV001032870

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 29, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From GeneDx, SCV000981066.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001032870.6

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

#	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: Sep 29, 2024

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