rs11941399

Variant names:

• chr4-166534341-G-A
• rs11941399

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 0.246 in 151,734 control chromosomes in the GnomAD database, including 8,801 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 0.25 (8801 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37192 AN: 151620 Hom.: 8760 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0547

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.246 AC: 37285 AN: 151734 Hom.: 8801 Cov.: 32 AF XY: 0.249 AC XY: 18411 AN XY: 74084

African (AFR) AF: 0.591 AC: 24447 AN: 41380

American (AMR) AF: 0.231 AC: 3527 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2575 AN: 5150

South Asian (SAS) AF: 0.191 AC: 913 AN: 4786

European-Finnish (FIN) AF: 0.0934 AC: 981 AN: 10508

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.0547 AC: 3713 AN: 67892

Other (OTH) AF: 0.226 AC: 476 AN: 2108

Alfa AF: 0.133 Hom.: 6631

Bravo AF: 0.273

Asia WGS AF: 0.354 AC: 1227 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs11941399; hg19: chr4-167455493;