rs11731298

Variant names:

• chr4-147691337-C-T
• rs11731298

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 0.0531 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0532 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

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0737

Gnomad4 EAS AF: 0.0953

Gnomad4 SAS AF: 0.0619

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0628 Hom.: 498

Bravo AF: 0.0446

Asia WGS AF: 0.0840 AC: 293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11731298; hg19: chr4-148612488;