rs11731298

chr4-147691337-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;