Variant 7-1057959-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001303473.2(GPR146):c.444C>T(p.Cys148Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00912 in 771,994 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0091 ( 11 hom., cov: 33)

Exomes 𝑓: 0.0091 ( 48 hom. )

Consequence

GPR146
NM_001303473.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.283

Variant links:

Genes affected

GPR146 (HGNC:21718): (G protein-coupled receptor 146) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

GPR146 links:

C7orf50 (HGNC:22421): (chromosome 7 open reading frame 50) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

C7orf50 links:

ENSG00000257607 (HGNC:):

ENSG00000257607 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 7-1057959-C-T is Benign according to our data. Variant chr7-1057959-C-T is described in ClinVar as [Benign]. Clinvar id is 773473.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.283 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR146	NM_001303473.2 linkuse as main transcript	c.444C>T	p.Cys148Cys	synonymous_variant	2/2	ENST00000444847.2	NP_001290402.1	Q96CH1A4D2Q3B4DTD6
C7orf50	NM_001318252.2 linkuse as main transcript	c.130-47816G>A		intron_variant		ENST00000397098.8	NP_001305181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR146	ENST00000444847.2 linkuse as main transcript	c.444C>T	p.Cys148Cys	synonymous_variant	2/2	2	NM_001303473.2	ENSP00000410743.2		Q96CH1
C7orf50	ENST00000397098.8 linkuse as main transcript	c.130-47816G>A		intron_variant		1	NM_001318252.2	ENSP00000380286.3		Q9BRJ6

Frequencies

GnomAD3 genomes

AF:

0.00914

AC:

1391

AN:

152240

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00200

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00713

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00165

Gnomad FIN

AF:

0.0339

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0116

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.00807

AC:

1973

AN:

244576

Hom.:

AF XY:

0.00837

AC XY:

1113

AN XY:

132986

show subpopulations

Gnomad AFR exome

AF:

0.00167

Gnomad AMR exome

AF:

0.00602

Gnomad ASJ exome

AF:

0.00209

Gnomad EAS exome

AF:

0.0000545

Gnomad SAS exome

AF:

0.00114

Gnomad FIN exome

AF:

0.0295

Gnomad NFE exome

AF:

0.0102

Gnomad OTH exome

AF:

0.0107

GnomAD4 exome

AF:

0.00912

AC:

5648

AN:

619636

Hom.:

Cov.:

AF XY:

0.00889

AC XY:

3009

AN XY:

338408

show subpopulations

Gnomad4 AFR exome

AF:

0.00198

Gnomad4 AMR exome

AF:

0.00601

Gnomad4 ASJ exome

AF:

0.00262

Gnomad4 EAS exome

AF:

0.0000555

Gnomad4 SAS exome

AF:

0.00132

Gnomad4 FIN exome

AF:

0.0278

Gnomad4 NFE exome

AF:

0.0104

Gnomad4 OTH exome

AF:

0.00935

GnomAD4 genome

AF:

0.00913

AC:

1391

AN:

152358

Hom.:

Cov.:

AF XY:

0.0102

AC XY:

761

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00200

Gnomad4 AMR

AF:

0.00712

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0339

Gnomad4 NFE

AF:

0.0116

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00896

Hom.:

Bravo

AF:

0.00666

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

0.85

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over