chr11-121373007-C-T

Variant names:

• chr11-121373007-C-T
• rs72991

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 0.646 in 152,014 control chromosomes in the GnomAD database, including 33,415 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 0.65 (33415 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.646 AC: 98131 AN: 151896 Hom.: 33404 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.646 AC: 98169 AN: 152014 Hom.: 33415 Cov.: 31 AF XY: 0.650 AC XY: 48289 AN XY: 74310

African (AFR) AF: 0.415 AC: 17179 AN: 41438

American (AMR) AF: 0.754 AC: 11527 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2494 AN: 3472

East Asian (EAS) AF: 0.828 AC: 4270 AN: 5158

South Asian (SAS) AF: 0.691 AC: 3331 AN: 4818

European-Finnish (FIN) AF: 0.736 AC: 7774 AN: 10566

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49446 AN: 67970

Other (OTH) AF: 0.674 AC: 1423 AN: 2110

Alfa AF: 0.702 Hom.: 110933

Bravo AF: 0.642

Asia WGS AF: 0.783 AC: 2722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.58
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs72991; hg19: chr11-121243716;