15-32703097-C-A

Variant names:

• chr15-32703097-C-A
• rs16970016

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 0.213 in 152,110 control chromosomes in the GnomAD database, including 4,493 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 0.21 (4493 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.213 AC: 32383 AN: 151992 Hom.: 4497 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.213 AC: 32388 AN: 152110 Hom.: 4493 Cov.: 33 AF XY: 0.223 AC XY: 16565 AN XY: 74346

African (AFR) AF: 0.167 AC: 6929 AN: 41522

American (AMR) AF: 0.220 AC: 3363 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3893 AN: 5170

South Asian (SAS) AF: 0.386 AC: 1857 AN: 4812

European-Finnish (FIN) AF: 0.283 AC: 2986 AN: 10544

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12360 AN: 67984

Other (OTH) AF: 0.204 AC: 430 AN: 2108

Alfa AF: 0.187 Hom.: 3847

Bravo AF: 0.204

Asia WGS AF: 0.530 AC: 1841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.12
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs16970016; hg19: chr15-32995298;