rs4406791

Variant names:

• chr11-92988621-A-C
• rs4406791

Your query was ambiguous. Multiple possible variants found:

• chr11-92988621-A-C
• chr11-92988621-A-G
• chr11-92988621-A-T

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 0.557 in 151,918 control chromosomes in the GnomAD database, including 23,939 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 0.56 (23939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.557 AC: 84560 AN: 151800 Hom.: 23907 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.557 AC: 84655 AN: 151918 Hom.: 23939 Cov.: 32 AF XY: 0.565 AC XY: 41987 AN XY: 74264

African (AFR) AF: 0.559 AC: 23146 AN: 41420

American (AMR) AF: 0.657 AC: 10027 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1521 AN: 3466

East Asian (EAS) AF: 0.695 AC: 3599 AN: 5176

South Asian (SAS) AF: 0.688 AC: 3311 AN: 4810

European-Finnish (FIN) AF: 0.574 AC: 6060 AN: 10550

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35062 AN: 67934

Other (OTH) AF: 0.541 AC: 1142 AN: 2110

Alfa AF: 0.432 Hom.: 1314

Bravo AF: 0.565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.75
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4406791; hg19: chr11-92721787;