chr11-61867728-T-C

Variant names:

• chr11-61867728-T-C
• rs17831757

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 0.0916 in 152,248 control chromosomes in the GnomAD database, including 780 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 0.092 (780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 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: 0.0916 AC: 13939 AN: 152130 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0916 AC: 13942 AN: 152248 Hom.: 780 Cov.: 32 AF XY: 0.0913 AC XY: 6798 AN XY: 74454

Gnomad4 AFR AF: 0.0467

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.00908

Gnomad4 SAS AF: 0.0481

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.107 Hom.: 125

Bravo AF: 0.0870

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17831757; hg19: chr11-61635200;