11-100641161-T-C

Position:

• chr11-100641161-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 0.439 in 138,488 control chromosomes in the GnomAD database, including 12,822 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 0.44 (12822 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.851

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100641161T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.439 AC: 60695 AN: 138388 Hom.: 12809 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.439 AC: 60742 AN: 138488 Hom.: 12822 Cov.: 31 AF XY: 0.446 AC XY: 30047 AN XY: 67380

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.414

Alfa AF: 0.403 Hom.: 1546

Bravo AF: 0.400

Asia WGS AF: 0.552 AC: 1904 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs916482; hg19: chr11-100511892;