11-121373007-C-T

Position:

• chr11-121373007-C-T

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 0.646 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.674

Alfa AF: 0.722 Hom.: 68331

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72991; hg19: chr11-121243716;