rs3758641

Variant names:

• chr11-33892916-G-A
• rs3758641

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 0.427 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.288 AC: 11928 AN: 41484

American (AMR) AF: 0.412 AC: 6291 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1463 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3033 AN: 5166

South Asian (SAS) AF: 0.475 AC: 2291 AN: 4820

European-Finnish (FIN) AF: 0.535 AC: 5658 AN: 10566

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32665 AN: 67958

Other (OTH) AF: 0.433 AC: 912 AN: 2108

Alfa AF: 0.386 Hom.: 4840

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs3758641; hg19: chr11-33914463;