Variant 7-1057638-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.123C>T(p.Gly41Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00691 in 770,380 control chromosomes in the GnomAD database, including 31 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0073 ( 28 hom. )

Consequence

GPR146
NM_001303473.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.71

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:

C7orf50 (HGNC:):

C7orf50 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 7-1057638-C-T is Benign according to our data. Variant chr7-1057638-C-T is described in ClinVar as [Benign]. Clinvar id is 770731.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.71 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR146	NM_001303473.2 linkuse as main transcript	c.123C>T	p.Gly41Gly	synonymous_variant	2/2	ENST00000444847.2	NP_001290402.1	Q96CH1A4D2Q3B4DTD6
C7orf50	NM_001318252.2 linkuse as main transcript	c.130-47495G>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.123C>T	p.Gly41Gly	synonymous_variant	2/2	2	NM_001303473.2	ENSP00000410743.2		Q96CH1
C7orf50	ENST00000397098.8 linkuse as main transcript	c.130-47495G>A		intron_variant		1	NM_001318252.2	ENSP00000380286.3		Q9BRJ6

Frequencies

GnomAD3 genomes

AF:

0.00541

AC:

823

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00118

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00451

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00518

Gnomad FIN

AF:

0.00885

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00735

Gnomad OTH

AF:

0.00718

GnomAD3 exomes

AF:

0.00647

AC:

1513

AN:

233688

Hom.:

AF XY:

0.00683

AC XY:

870

AN XY:

127376

show subpopulations

Gnomad AFR exome

AF:

0.00114

Gnomad AMR exome

AF:

0.00431

Gnomad ASJ exome

AF:

0.0169

Gnomad EAS exome

AF:

0.0000570

Gnomad SAS exome

AF:

0.00600

Gnomad FIN exome

AF:

0.00696

Gnomad NFE exome

AF:

0.00792

Gnomad OTH exome

AF:

0.00901

GnomAD4 exome

AF:

0.00729

AC:

4503

AN:

618048

Hom.:

Cov.:

AF XY:

0.00724

AC XY:

2439

AN XY:

336952

show subpopulations

Gnomad4 AFR exome

AF:

0.00136

Gnomad4 AMR exome

AF:

0.00427

Gnomad4 ASJ exome

AF:

0.0182

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00549

Gnomad4 FIN exome

AF:

0.00760

Gnomad4 NFE exome

AF:

0.00822

Gnomad4 OTH exome

AF:

0.00795

GnomAD4 genome

AF:

0.00541

AC:

824

AN:

152332

Hom.:

Cov.:

AF XY:

0.00561

AC XY:

418

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00118

Gnomad4 AMR

AF:

0.00451

Gnomad4 ASJ

AF:

0.0179

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.00885

Gnomad4 NFE

AF:

0.00735

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00719

Hom.:

Bravo

AF:

0.00492

Asia WGS

AF:

0.00491

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

5.3

DANN

Benign

0.54

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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