13-113872798-T-G

Variant names:

• chr13-113872798-T-G
• rs9550270
• ENST00000757209.1:n.224+6887T>G

Variant summary

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

The ENST00000757209.1(GAS6-DT):​n.224+6887T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,032 control chromosomes in the GnomAD database, including 5,629 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 0.27 (5629 hom., cov: 33)
• Consequence: GAS6-DT ENST00000757209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 6 publications found

Genes affected

GAS6-DT (HGNC:43694): (GAS6 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAS6-DT	ENST00000757209.1	n.224+6887T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40804 AN: 151914 Hom.: 5629 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.257

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.268 AC: 40803 AN: 152032 Hom.: 5629 Cov.: 33 AF XY: 0.268 AC XY: 19885 AN XY: 74318

African (AFR) AF: 0.203 AC: 8405 AN: 41504

American (AMR) AF: 0.326 AC: 4976 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 824 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1893 AN: 5176

South Asian (SAS) AF: 0.179 AC: 865 AN: 4826

European-Finnish (FIN) AF: 0.307 AC: 3236 AN: 10538

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19772 AN: 67940

Other (OTH) AF: 0.256 AC: 539 AN: 2108

Alfa AF: 0.268 Hom.: 3876

Bravo AF: 0.274

Asia WGS AF: 0.223 AC: 776 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.45
PhyloP100		0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9550270; hg19: chr13-114575771;