Variant chr17-65053580-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_006572.6(GNA13):c.432A>G(p.Gln144=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,613,844 control chromosomes in the GnomAD database, including 154 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0097 ( 5 hom., cov: 33)

Exomes 𝑓: 0.013 ( 149 hom. )

Consequence

GNA13
NM_006572.6 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.01

Variant links:

Genes affected

GNA13 (HGNC:4381): (G protein subunit alpha 13) Predicted to enable D5 dopamine receptor binding activity; G-protein beta/gamma-subunit complex binding activity; and GTPase activity. Predicted to be involved in several processes, including Rho protein signal transduction; activation of phospholipase D activity; and multicellular organism aging. Predicted to act upstream of or within several processes, including branching involved in blood vessel morphogenesis; negative regulation of vascular associated smooth muscle cell migration; and negative regulation of vascular associated smooth muscle cell proliferation. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

GNA13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 17-65053580-T-C is Benign according to our data. Variant chr17-65053580-T-C is described in ClinVar as [Benign]. Clinvar id is 789341.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.01 with no splicing effect.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00965 (1470/152326) while in subpopulation AMR AF= 0.024 (367/15292). AF 95% confidence interval is 0.022. There are 5 homozygotes in gnomad4. There are 685 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1470 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNA13	NM_006572.6 linkuse as main transcript	c.432A>G	p.Gln144=	synonymous_variant	2/4	ENST00000439174.7
GNA13	NM_001282425.2 linkuse as main transcript	c.147A>G	p.Gln49=	synonymous_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNA13	ENST00000439174.7 linkuse as main transcript	c.432A>G	p.Gln144=	synonymous_variant	2/4	1	NM_006572.6	P1	Q14344-1
GNA13	ENST00000541118.1 linkuse as main transcript	c.147A>G	p.Gln49=	synonymous_variant	2/4	2			Q14344-2

Frequencies

GnomAD3 genomes

AF:

0.00964

AC:

1467

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00297

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0239

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00443

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0131

Gnomad OTH

AF:

0.00860

GnomAD3 exomes

AF:

0.0110

AC:

2756

AN:

251494

Hom.:

AF XY:

0.00998

AC XY:

1356

AN XY:

135922

show subpopulations

Gnomad AFR exome

AF:

0.00265

Gnomad AMR exome

AF:

0.0272

Gnomad ASJ exome

AF:

0.00387

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00327

Gnomad FIN exome

AF:

0.00508

Gnomad NFE exome

AF:

0.0127

Gnomad OTH exome

AF:

0.0121

GnomAD4 exome

AF:

0.0127

AC:

18619

AN:

1461518

Hom.:

149

Cov.:

AF XY:

0.0123

AC XY:

8939

AN XY:

727106

show subpopulations

Gnomad4 AFR exome

AF:

0.00191

Gnomad4 AMR exome

AF:

0.0256

Gnomad4 ASJ exome

AF:

0.00432

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00351

Gnomad4 FIN exome

AF:

0.00578

Gnomad4 NFE exome

AF:

0.0145

Gnomad4 OTH exome

AF:

0.00967

GnomAD4 genome

AF:

0.00965

AC:

1470

AN:

152326

Hom.:

Cov.:

AF XY:

0.00920

AC XY:

685

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.00296

Gnomad4 AMR

AF:

0.0240

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00443

Gnomad4 NFE

AF:

0.0131

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.0105

Hom.:

Bravo

AF:

0.0111

Asia WGS

AF:

0.00289

AC:

AN:

3478

EpiCase

AF:

0.0117

EpiControl

AF:

0.0121

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

DANN

Benign

0.69

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