Variant 12-100623990-G-A 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_174942.3(GAS2L3):c.1185G>A(p.Pro395=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00572 in 1,613,814 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 0.0041 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0059 ( 41 hom. )

Consequence

GAS2L3
NM_174942.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0330

Variant links:

Genes affected

GAS2L3 (HGNC:27475): (growth arrest specific 2 like 3) Enables actin binding activity and microtubule binding activity. Involved in actin cytoskeleton organization and microtubule cytoskeleton organization. Located in actin cytoskeleton and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

GAS2L3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

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

BP6

Variant 12-100623990-G-A is Benign according to our data. Variant chr12-100623990-G-A is described in ClinVar as [Benign]. Clinvar id is 770988.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.033 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS2L3	NM_174942.3 linkuse as main transcript	c.1185G>A	p.Pro395=	synonymous_variant	10/10	ENST00000547754.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS2L3	ENST00000547754.6 linkuse as main transcript	c.1185G>A	p.Pro395=	synonymous_variant	10/10	1	NM_174942.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00412

AC:

626

AN:

151926

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00282

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00313

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00725

Gnomad OTH

AF:

0.00288

GnomAD3 exomes

AF:

0.00433

AC:

1086

AN:

250910

Hom.:

AF XY:

0.00409

AC XY:

554

AN XY:

135562

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00194

Gnomad ASJ exome

AF:

0.00169

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000229

Gnomad FIN exome

AF:

0.00374

Gnomad NFE exome

AF:

0.00767

Gnomad OTH exome

AF:

0.00425

GnomAD4 exome

AF:

0.00589

AC:

8607

AN:

1461770

Hom.:

Cov.:

AF XY:

0.00582

AC XY:

4234

AN XY:

727188

show subpopulations

Gnomad4 AFR exome

AF:

0.000926

Gnomad4 AMR exome

AF:

0.00201

Gnomad4 ASJ exome

AF:

0.00230

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000255

Gnomad4 FIN exome

AF:

0.00453

Gnomad4 NFE exome

AF:

0.00710

Gnomad4 OTH exome

AF:

0.00444

GnomAD4 genome

AF:

0.00412

AC:

626

AN:

152044

Hom.:

Cov.:

AF XY:

0.00384

AC XY:

285

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.00116

Gnomad4 AMR

AF:

0.00282

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00313

Gnomad4 NFE

AF:

0.00725

Gnomad4 OTH

AF:

0.00285

Alfa

AF:

0.00510

Hom.:

Bravo

AF:

0.00388

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00638

EpiControl

AF:

0.00557

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

Invitae

Nov 17, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

DANN

Benign

0.39

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