15-74833304-A-C

Variant names:

• chr15-74833304-A-C
• rs6495122

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 0.433 in 152,106 control chromosomes in the GnomAD database, including 15,836 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 0.43 (15836 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 97 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65791 AN: 151988 Hom.: 15835 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.433 AC: 65814 AN: 152106 Hom.: 15836 Cov.: 33 AF XY: 0.420 AC XY: 31208 AN XY: 74348

African (AFR) AF: 0.276 AC: 11444 AN: 41500

American (AMR) AF: 0.441 AC: 6738 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3470

East Asian (EAS) AF: 0.173 AC: 896 AN: 5182

South Asian (SAS) AF: 0.148 AC: 713 AN: 4824

European-Finnish (FIN) AF: 0.468 AC: 4941 AN: 10568

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38115 AN: 67968

Other (OTH) AF: 0.426 AC: 902 AN: 2116

Alfa AF: 0.516 Hom.: 102136

Bravo AF: 0.431

Asia WGS AF: 0.158 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.50
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6495122; hg19: chr15-75125645; COSMIC: COSV67663653;