chr11-97687762-C-T

Position:

• chr11-97687762-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 0.925 in 152,258 control chromosomes in the GnomAD database, including 65,815 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 0.93 (65815 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

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 = 0.979 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: 0.926 AC: 140820 AN: 152140 Hom.: 65783 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.985

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.939

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

GnomAD4 genome AF: 0.925 AC: 140904 AN: 152258 Hom.: 65815 Cov.: 33 AF XY: 0.927 AC XY: 69007 AN XY: 74452

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.981

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.986

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.939

Alfa AF: 0.951 Hom.: 8079

Bravo AF: 0.914

Asia WGS AF: 0.977 AC: 3377 AN: 3456

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	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs670687; hg19: chr11-97558762;