Variant rs1803628 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000327773.7(GAS6):c.1332C>T(p.Cys444=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 1,612,610 control chromosomes in the GnomAD database, including 15,772 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2505 hom., cov: 31)

Exomes 𝑓: 0.12 ( 13267 hom. )

Consequence

GAS6
ENST00000327773.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0490

Variant links:

Genes affected

GAS6 (HGNC:4168): (growth arrest specific 6) This gene encodes a gamma-carboxyglutamic acid (Gla)-containing protein thought to be involved in the stimulation of cell proliferation. This gene is frequently overexpressed in many cancers and has been implicated as an adverse prognostic marker. Elevated protein levels are additionally associated with a variety of disease states, including venous thromboembolic disease, systemic lupus erythematosus, chronic renal failure, and preeclampsia. [provided by RefSeq, Aug 2014]

GAS6 links:

GAS6-AS1 (HGNC:39826): (GAS6 antisense RNA 1)

GAS6-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP7

Synonymous conserved (PhyloP=0.049 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAS6	NM_000820.4 linkuse as main transcript	c.1332C>T	p.Cys444=	synonymous_variant	12/15	ENST00000327773.7	NP_000811.1
GAS6-AS1	NR_044995.2 linkuse as main transcript	n.83-6351G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAS6	ENST00000327773.7 linkuse as main transcript	c.1332C>T	p.Cys444=	synonymous_variant	12/15	1	NM_000820.4	ENSP00000331831	P1	Q14393-2
GAS6-AS1	ENST00000458001.2 linkuse as main transcript	n.63-6351G>A		intron_variant, non_coding_transcript_variant		5
GAS6	ENST00000480426.5 linkuse as main transcript	n.1487C>T		non_coding_transcript_exon_variant	4/7	2
GAS6	ENST00000610073.1 linkuse as main transcript	n.1152C>T		non_coding_transcript_exon_variant	6/9	2

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24797

AN:

151758

Hom.:

2493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.0646

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.303

Gnomad FIN

AF:

0.0988

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0947

Gnomad OTH

AF:

0.137

GnomAD3 exomes

AF:

0.161

AC:

40254

AN:

250312

Hom.:

4378

AF XY:

0.158

AC XY:

21460

AN XY:

135608

show subpopulations

Gnomad AFR exome

AF:

0.285

Gnomad AMR exome

AF:

0.266

Gnomad ASJ exome

AF:

0.0638

Gnomad EAS exome

AF:

0.209

Gnomad SAS exome

AF:

0.290

Gnomad FIN exome

AF:

0.0925

Gnomad NFE exome

AF:

0.0911

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.118

AC:

172208

AN:

1460734

Hom.:

13267

Cov.:

AF XY:

0.121

AC XY:

88216

AN XY:

726662

show subpopulations

Gnomad4 AFR exome

AF:

0.284

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.0643

Gnomad4 EAS exome

AF:

0.210

Gnomad4 SAS exome

AF:

0.286

Gnomad4 FIN exome

AF:

0.0928

Gnomad4 NFE exome

AF:

0.0930

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.163

AC:

24830

AN:

151876

Hom.:

2505

Cov.:

AF XY:

0.166

AC XY:

12311

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.276

Gnomad4 AMR

AF:

0.186

Gnomad4 ASJ

AF:

0.0646

Gnomad4 EAS

AF:

0.206

Gnomad4 SAS

AF:

0.301

Gnomad4 FIN

AF:

0.0988

Gnomad4 NFE

AF:

0.0947

Gnomad4 OTH

AF:

0.145

Alfa

AF:

0.114

Hom.:

717

Bravo

AF:

0.174

Asia WGS

AF:

0.314

AC:

1092

AN:

3478

EpiCase

AF:

0.0862

EpiControl

AF:

0.0865

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

6.1

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over