15-70506220-C-T

Variant names:

• chr15-70506220-C-T
• rs8034004

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 152,132 control chromosomes in the GnomAD database, including 17,286 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 (17286 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) 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: 0.433 AC: 65880 AN: 152014 Hom.: 17295 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.433 AC: 65860 AN: 152132 Hom.: 17286 Cov.: 33 AF XY: 0.438 AC XY: 32580 AN XY: 74356

African (AFR) AF: 0.119 AC: 4943 AN: 41534

American (AMR) AF: 0.528 AC: 8071 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2058 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3361 AN: 5182

South Asian (SAS) AF: 0.406 AC: 1960 AN: 4826

European-Finnish (FIN) AF: 0.588 AC: 6213 AN: 10562

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37500 AN: 67952

Other (OTH) AF: 0.467 AC: 988 AN: 2114

Alfa AF: 0.516 Hom.: 33353

Bravo AF: 0.418

Asia WGS AF: 0.506 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.9
DANN	Benign	0.71
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs8034004; hg19: chr15-70798559;