11-80689603-T-C

Position:

• chr11-80689603-T-C

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 0.546 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.546

Alfa AF: 0.594 Hom.: 3561

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501474; hg19: chr11-80400647;