rs4774925

Variant names:

• chr15-57312204-T-C
• rs4774925

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 0.554 in 152,104 control chromosomes in the GnomAD database, including 24,863 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 0.55 (24863 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 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: 0.554 AC: 84272 AN: 151986 Hom.: 24862 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.554 AC: 84317 AN: 152104 Hom.: 24863 Cov.: 33 AF XY: 0.560 AC XY: 41608 AN XY: 74342

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.554

Alfa AF: 0.611 Hom.: 16979

Bravo AF: 0.541

Asia WGS AF: 0.525 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.22
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4774925; hg19: chr15-57604402;