Variant 10-123666737-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_153442.4(GPR26):c.330C>T(p.Phe110Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00608 in 1,598,366 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0046 ( 6 hom., cov: 34)

Exomes 𝑓: 0.0062 ( 39 hom. )

Consequence

GPR26
NM_153442.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0180

Variant links:

Genes affected

GPR26 (HGNC:4481): (G protein-coupled receptor 26) This gene encodes a G protein-couple receptor protein. G-protein-coupled receptors are a large family of membrane proteins that are involved in cellular responses to environmental stimuli, neurotransmitters, and hormones. The encoded protein may play a role in neurodegenerative diseases. Epigenetic silencing of this gene has been observed in gliomas. [provided by RefSeq, Sep 2016]

GPR26 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 10-123666737-C-T is Benign according to our data. Variant chr10-123666737-C-T is described in ClinVar as [Benign]. Clinvar id is 788827.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.018 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR26	NM_153442.4 linkuse as main transcript	c.330C>T	p.Phe110Phe	synonymous_variant	1/3	ENST00000284674.2	NP_703143.1	Q8NDV2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR26	ENST00000284674.2 linkuse as main transcript	c.330C>T	p.Phe110Phe	synonymous_variant	1/3	1	NM_153442.4	ENSP00000284674.1		Q8NDV2

Frequencies

GnomAD3 genomes

AF:

0.00459

AC:

698

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00106

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.00518

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.00889

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00681

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00453

AC:

988

AN:

218282

Hom.:

AF XY:

0.00478

AC XY:

577

AN XY:

120692

show subpopulations

Gnomad AFR exome

AF:

0.000690

Gnomad AMR exome

AF:

0.00262

Gnomad ASJ exome

AF:

0.00305

Gnomad EAS exome

AF:

0.000656

Gnomad SAS exome

AF:

0.00685

Gnomad FIN exome

AF:

0.00113

Gnomad NFE exome

AF:

0.00626

Gnomad OTH exome

AF:

0.00529

GnomAD4 exome

AF:

0.00623

AC:

9015

AN:

1446064

Hom.:

Cov.:

AF XY:

0.00619

AC XY:

4449

AN XY:

719320

show subpopulations

Gnomad4 AFR exome

AF:

0.000601

Gnomad4 AMR exome

AF:

0.00285

Gnomad4 ASJ exome

AF:

0.00316

Gnomad4 EAS exome

AF:

0.000280

Gnomad4 SAS exome

AF:

0.00725

Gnomad4 FIN exome

AF:

0.00154

Gnomad4 NFE exome

AF:

0.00695

Gnomad4 OTH exome

AF:

0.00557

GnomAD4 genome

AF:

0.00458

AC:

698

AN:

152302

Hom.:

Cov.:

AF XY:

0.00399

AC XY:

297

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00106

Gnomad4 AMR

AF:

0.00248

Gnomad4 ASJ

AF:

0.00518

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.00890

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00681

Gnomad4 OTH

AF:

0.00614

Alfa

AF:

0.00573

Hom.:

Bravo

AF:

0.00433

Asia WGS

AF:

0.000867

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

9.0

DANN

Benign

0.94

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