rs1931336

Variant names:

• chr13-108179885-G-A
• rs1931336

Your query was ambiguous. Multiple possible variants found:

• chr13-108179885-G-A
• chr13-108179885-G-C
• chr13-108179885-G-T

Variant summary

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

The variant allele was found at a frequency of 0.846 in 152,102 control chromosomes in the GnomAD database, including 54,507 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 0.85 (54507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.862 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

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128540 AN: 151984 Hom.: 54468 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.846 AC: 128634 AN: 152102 Hom.: 54507 Cov.: 32 AF XY: 0.849 AC XY: 63129 AN XY: 74386

African (AFR) AF: 0.789 AC: 32710 AN: 41482

American (AMR) AF: 0.866 AC: 13234 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2953 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4270 AN: 5170

South Asian (SAS) AF: 0.880 AC: 4246 AN: 4826

European-Finnish (FIN) AF: 0.882 AC: 9308 AN: 10550

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59029 AN: 68010

Other (OTH) AF: 0.854 AC: 1801 AN: 2110

Alfa AF: 0.856 Hom.: 99851

Bravo AF: 0.839

Asia WGS AF: 0.823 AC: 2844 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	10
DANN	Benign	0.31
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1931336; hg19: chr13-108832233;