rs1917858

Variant names:

• chr11-80691343-T-A
• rs1917858

Your query was ambiguous. Multiple possible variants found:

• chr11-80691343-T-A
• chr11-80691343-T-G

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 0.533 in 151,912 control chromosomes in the GnomAD database, including 25,065 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 0.53 (25065 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 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: 0.533 AC: 80943 AN: 151794 Hom.: 25049 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.533 AC: 80976 AN: 151912 Hom.: 25065 Cov.: 32 AF XY: 0.538 AC XY: 39931 AN XY: 74252

African (AFR) AF: 0.207 AC: 8577 AN: 41488

American (AMR) AF: 0.674 AC: 10265 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2094 AN: 3466

East Asian (EAS) AF: 0.333 AC: 1715 AN: 5154

South Asian (SAS) AF: 0.729 AC: 3507 AN: 4812

European-Finnish (FIN) AF: 0.655 AC: 6939 AN: 10586

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45938 AN: 67864

Other (OTH) AF: 0.535 AC: 1128 AN: 2108

Alfa AF: 0.587 Hom.: 3509

Bravo AF: 0.516

Asia WGS AF: 0.538 AC: 1868 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs1917858; hg19: chr11-80402387; COSMIC: COSV69021277;