rs3758641

chr11-33892916-G-A

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 0.427 in 152,044 control chromosomes in the GnomAD database, including 14,533 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 0.43 (14533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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: 0.427 AC: 64917 AN: 151926 Hom.: 14542 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.427 AC: 64914 AN: 152044 Hom.: 14533 Cov.: 32 AF XY: 0.431 AC XY: 32011 AN XY: 74330

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.433

Alfa AF: 0.421 Hom.: 2070

Bravo AF: 0.414

Asia WGS AF: 0.464 AC: 1612 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	1.2
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758641; hg19: chr11-33914463;