15-70506220-C-T

Position:

• chr15-70506220-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.467

Alfa AF: 0.531 Hom.: 21449

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8034004; hg19: chr15-70798559;