11-91575535-C-T

Variant names:

• chr11-91575535-C-T
• rs1022362

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 0.529 in 151,836 control chromosomes in the GnomAD database, including 22,037 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 0.53 (22037 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.739 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: 0.529 AC: 80266 AN: 151714 Hom.: 22020 Cov.: 31

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.529 AC: 80315 AN: 151836 Hom.: 22037 Cov.: 31 AF XY: 0.535 AC XY: 39725 AN XY: 74198

African (AFR) AF: 0.402 AC: 16655 AN: 41390

American (AMR) AF: 0.640 AC: 9752 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1798 AN: 3472

East Asian (EAS) AF: 0.759 AC: 3895 AN: 5134

South Asian (SAS) AF: 0.467 AC: 2249 AN: 4818

European-Finnish (FIN) AF: 0.670 AC: 7067 AN: 10544

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37183 AN: 67926

Other (OTH) AF: 0.549 AC: 1154 AN: 2102

Alfa AF: 0.536 Hom.: 4413

Bravo AF: 0.524

Asia WGS AF: 0.600 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.54
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1022362; hg19: chr11-91308701;