11-2174751-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 0.641 in 152,122 control chromosomes in the GnomAD database, including 31,530 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 0.64 (31530 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 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: 0.641 AC: 97450 AN: 152004 Hom.: 31526 Cov.: 34

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.641 AC: 97478 AN: 152122 Hom.: 31530 Cov.: 34 AF XY: 0.649 AC XY: 48243 AN XY: 74388

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.685

Alfa AF: 0.637 Hom.: 42773

Bravo AF: 0.639

Asia WGS AF: 0.846 AC: 2939 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.5
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10743152; hg19: chr11-2195981; COSMIC: COSV60768768;