rs16969816

Variant names:

• chr15-32701444-G-A
• rs16969816

Your query was ambiguous. Multiple possible variants found:

• chr15-32701444-G-A
• chr15-32701444-G-C

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 0.252 in 152,162 control chromosomes in the GnomAD database, including 5,620 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 0.25 (5620 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.252 AC: 38335 AN: 152044 Hom.: 5590 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.252 AC: 38412 AN: 152162 Hom.: 5620 Cov.: 33 AF XY: 0.257 AC XY: 19086 AN XY: 74382

African (AFR) AF: 0.387 AC: 16072 AN: 41514

American (AMR) AF: 0.224 AC: 3430 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2124 AN: 5168

South Asian (SAS) AF: 0.340 AC: 1640 AN: 4824

European-Finnish (FIN) AF: 0.208 AC: 2204 AN: 10578

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11798 AN: 68008

Other (OTH) AF: 0.246 AC: 519 AN: 2114

Alfa AF: 0.205 Hom.: 9864

Bravo AF: 0.259

Asia WGS AF: 0.389 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs16969816; hg19: chr15-32993645;