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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.880

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.854

Alfa AF: 0.854 Hom.: 21684

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1931336; hg19: chr13-108832233;