chr11-80691598-T-C

Variant names:

• chr11-80691598-T-C
• rs1917857

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 151,822 control chromosomes in the GnomAD database, including 25,063 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 (25063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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: 80932 AN: 151704 Hom.: 25047 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.533 AC: 80965 AN: 151822 Hom.: 25063 Cov.: 32 AF XY: 0.538 AC XY: 39901 AN XY: 74174

African (AFR) AF: 0.207 AC: 8577 AN: 41452

American (AMR) AF: 0.674 AC: 10260 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2093 AN: 3460

East Asian (EAS) AF: 0.333 AC: 1716 AN: 5152

South Asian (SAS) AF: 0.729 AC: 3511 AN: 4818

European-Finnish (FIN) AF: 0.656 AC: 6925 AN: 10560

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

European-Non Finnish (NFE) AF: 0.677 AC: 45938 AN: 67850

Other (OTH) AF: 0.536 AC: 1132 AN: 2110

Alfa AF: 0.589 Hom.: 5004

Bravo AF: 0.516

Asia WGS AF: 0.539 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.9
DANN	Benign	0.64
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1917857; hg19: chr11-80402642;