chr13-113835487-C-T

Variant names:

• chr13-113835487-C-T
• rs7331124
• NM_000820.4:c.712+26G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000820.4(GAS6):​c.712+26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,609,196 control chromosomes in the GnomAD database, including 18,665 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 0.13 (1465 hom., cov: 32)
  • Exomes 𝑓: 0.15 (17200 hom.)
• Consequence: GAS6 NM_000820.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 7 publications found

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000820.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS6	NM_000820.4	MANE Select	c.712+26G>A		intron	N/A	NP_000811.1
	GAS6-AS1	NR_044995.2		n.251+723C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS6	ENST00000327773.7	TSL:1 MANE Select	c.712+26G>A		intron	N/A	ENSP00000331831.6
	GAS6-AS1	ENST00000458001.2	TSL:5	n.337+723C>T		intron	N/A
	GAS6	ENST00000610073.1	TSL:2	n.532+26G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20079 AN: 152022 Hom.: 1465 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0414

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.139

GnomAD2 exomes AF: 0.124 AC: 30612 AN: 246722 AF XY: 0.124

Gnomad AFR exome AF: 0.0893

Gnomad AMR exome AF: 0.0835

Gnomad ASJ exome AF: 0.281

Gnomad EAS exome AF: 0.00126

Gnomad FIN exome AF: 0.147

Gnomad NFE exome AF: 0.164

Gnomad OTH exome AF: 0.146

GnomAD4 exome AF: 0.146 AC: 213262 AN: 1457058 Hom.: 17200 Cov.: 32 AF XY: 0.144 AC XY: 104405 AN XY: 724422

African (AFR) AF: 0.0927 AC: 3098 AN: 33404

American (AMR) AF: 0.0895 AC: 3986 AN: 44516

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 7323 AN: 26050

East Asian (EAS) AF: 0.000656 AC: 26 AN: 39642

South Asian (SAS) AF: 0.0465 AC: 4003 AN: 86046

European-Finnish (FIN) AF: 0.149 AC: 7750 AN: 51898

Middle Eastern (MID) AF: 0.137 AC: 780 AN: 5692

European-Non Finnish (NFE) AF: 0.160 AC: 177394 AN: 1109592

Other (OTH) AF: 0.148 AC: 8902 AN: 60218

GnomAD4 genome AF: 0.132 AC: 20077 AN: 152138 Hom.: 1465 Cov.: 32 AF XY: 0.129 AC XY: 9608 AN XY: 74382

African (AFR) AF: 0.0960 AC: 3985 AN: 41504

American (AMR) AF: 0.124 AC: 1899 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 970 AN: 3472

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5170

South Asian (SAS) AF: 0.0412 AC: 199 AN: 4830

European-Finnish (FIN) AF: 0.145 AC: 1542 AN: 10598

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10968 AN: 67958

Other (OTH) AF: 0.138 AC: 290 AN: 2106

Alfa AF: 0.144 Hom.: 657

Bravo AF: 0.129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.024
DANN	Benign	0.91
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7331124; hg19: chr13-114538460;