chr11-80689603-T-C

Variant names:

• chr11-80689603-T-C
• rs10501474

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 0.546 in 151,870 control chromosomes in the GnomAD database, including 25,556 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 0.55 (25556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 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: 0.546 AC: 82846 AN: 151752 Hom.: 25542 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.546 AC: 82879 AN: 151870 Hom.: 25556 Cov.: 32 AF XY: 0.550 AC XY: 40781 AN XY: 74208

African (AFR) AF: 0.249 AC: 10299 AN: 41432

American (AMR) AF: 0.679 AC: 10346 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2097 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1717 AN: 5140

South Asian (SAS) AF: 0.729 AC: 3509 AN: 4816

European-Finnish (FIN) AF: 0.655 AC: 6903 AN: 10536

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46043 AN: 67926

Other (OTH) AF: 0.546 AC: 1150 AN: 2106

Alfa AF: 0.580 Hom.: 3574

Bravo AF: 0.530

Asia WGS AF: 0.540 AC: 1877 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.68
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10501474; hg19: chr11-80400647;