rs11731298

Variant names:

• chr4-147691337-C-T
• rs11731298

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 0.0531 in 152,244 control chromosomes in the GnomAD database, including 297 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 0.053 (297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0884 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0532 AC: 8088 AN: 152126 Hom.: 297 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0751

Gnomad AMR AF: 0.0423

Gnomad ASJ AF: 0.0737

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0531 AC: 8081 AN: 152244 Hom.: 297 Cov.: 32 AF XY: 0.0556 AC XY: 4135 AN XY: 74432

African (AFR) AF: 0.0118 AC: 492 AN: 41554

American (AMR) AF: 0.0423 AC: 646 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0737 AC: 256 AN: 3472

East Asian (EAS) AF: 0.0953 AC: 494 AN: 5184

South Asian (SAS) AF: 0.0619 AC: 299 AN: 4828

European-Finnish (FIN) AF: 0.109 AC: 1158 AN: 10588

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0663 AC: 4508 AN: 68018

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0585 Hom.: 732

Bravo AF: 0.0446

Asia WGS AF: 0.0840 AC: 293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.44
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs11731298; hg19: chr4-148612488;