chr11-91888669-T-C

Variant names:

• chr11-91888669-T-C
• rs961263

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.617 in 152,004 control chromosomes in the GnomAD database, including 30,032 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 0.62 (30032 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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: 0.617 AC: 93679 AN: 151886 Hom.: 30012 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.617 AC: 93752 AN: 152004 Hom.: 30032 Cov.: 31 AF XY: 0.623 AC XY: 46279 AN XY: 74292

African (AFR) AF: 0.436 AC: 18054 AN: 41420

American (AMR) AF: 0.656 AC: 10023 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2362 AN: 3468

East Asian (EAS) AF: 0.911 AC: 4702 AN: 5162

South Asian (SAS) AF: 0.798 AC: 3853 AN: 4828

European-Finnish (FIN) AF: 0.670 AC: 7095 AN: 10582

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45394 AN: 67950

Other (OTH) AF: 0.643 AC: 1357 AN: 2110

Alfa AF: 0.632 Hom.: 11946

Bravo AF: 0.608

Asia WGS AF: 0.795 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.5
DANN	Benign	0.53
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs961263; hg19: chr11-91621835;