11-35241591-A-G

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 0.801 in 152,180 control chromosomes in the GnomAD database, including 49,675 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 0.80 (49675 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 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: 0.801 AC: 121759 AN: 152062 Hom.: 49615 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.928

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.801 AC: 121882 AN: 152180 Hom.: 49675 Cov.: 32 AF XY: 0.805 AC XY: 59853 AN XY: 74382

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.928

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.800

Alfa AF: 0.707 Hom.: 3402

Bravo AF: 0.816

Asia WGS AF: 0.855 AC: 2969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.043
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4756201; hg19: chr11-35263138;