11-91575535-C-T

Position:

• chr11-91575535-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 0.529 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.549

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1022362; hg19: chr11-91308701;