rs1917858

chr11-80691343-T-Achr11-80691343-T-G

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 0.533 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.535

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

Splicing

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

Publications

LitVar

Other links and lift over

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