rs8025170

Variant names:

• chr15-74878642-G-A
• rs8025170

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 0.218 in 152,060 control chromosomes in the GnomAD database, including 4,435 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 (4435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33205 AN: 151942 Hom.: 4440 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.218 AC: 33215 AN: 152060 Hom.: 4435 Cov.: 32 AF XY: 0.227 AC XY: 16840 AN XY: 74312

African (AFR) AF: 0.258 AC: 10709 AN: 41448

American (AMR) AF: 0.202 AC: 3087 AN: 15274

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

East Asian (EAS) AF: 0.621 AC: 3210 AN: 5172

South Asian (SAS) AF: 0.454 AC: 2186 AN: 4820

European-Finnish (FIN) AF: 0.214 AC: 2257 AN: 10558

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

European-Non Finnish (NFE) AF: 0.151 AC: 10263 AN: 67998

Other (OTH) AF: 0.230 AC: 485 AN: 2112

Alfa AF: 0.179 Hom.: 9257

Bravo AF: 0.218

Asia WGS AF: 0.550 AC: 1911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.57
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs8025170; hg19: chr15-75170983;