rs4774925

Variant names:

• chr15-57312204-T-C
• rs4774925

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 0.554 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.554 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

African (AFR) AF: 0.352 AC: 14601 AN: 41496

American (AMR) AF: 0.630 AC: 9625 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2090 AN: 3468

East Asian (EAS) AF: 0.456 AC: 2355 AN: 5164

South Asian (SAS) AF: 0.590 AC: 2843 AN: 4816

European-Finnish (FIN) AF: 0.718 AC: 7586 AN: 10560

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43206 AN: 67992

Other (OTH) AF: 0.554 AC: 1172 AN: 2116

Alfa AF: 0.603 Hom.: 22827

Bravo AF: 0.541

Asia WGS AF: 0.525 AC: 1828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.22
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4774925; hg19: chr15-57604402;