chr15-74884896-A-C

Variant names:

• chr15-74884896-A-C
• rs8029351

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 0.22 in 152,154 control chromosomes in the GnomAD database, including 4,550 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 0.22 (4550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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: 0.220 AC: 33424 AN: 152036 Hom.: 4555 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.220 AC: 33433 AN: 152154 Hom.: 4550 Cov.: 32 AF XY: 0.228 AC XY: 16955 AN XY: 74368

African (AFR) AF: 0.258 AC: 10726 AN: 41504

American (AMR) AF: 0.203 AC: 3097 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 630 AN: 3472

East Asian (EAS) AF: 0.649 AC: 3356 AN: 5168

South Asian (SAS) AF: 0.458 AC: 2206 AN: 4812

European-Finnish (FIN) AF: 0.213 AC: 2257 AN: 10574

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10286 AN: 68020

Other (OTH) AF: 0.231 AC: 488 AN: 2112

Alfa AF: 0.185 Hom.: 493

Bravo AF: 0.219

Asia WGS AF: 0.567 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.36
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs8029351; hg19: chr15-75177237;