11-97687762-C-T

Variant names:

• chr11-97687762-C-T
• rs670687

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;