15-32701800-A-G

Variant names:

• chr15-32701800-A-G
• rs16969862

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 0.136 in 152,200 control chromosomes in the GnomAD database, including 1,694 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 0.14 (1694 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 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: 0.136 AC: 20683 AN: 152082 Hom.: 1690 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0711

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.136 AC: 20700 AN: 152200 Hom.: 1694 Cov.: 33 AF XY: 0.142 AC XY: 10532 AN XY: 74406

African (AFR) AF: 0.156 AC: 6499 AN: 41530

American (AMR) AF: 0.150 AC: 2299 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0711 AC: 247 AN: 3472

East Asian (EAS) AF: 0.387 AC: 2001 AN: 5164

South Asian (SAS) AF: 0.298 AC: 1438 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1223 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0967 AC: 6579 AN: 68018

Other (OTH) AF: 0.138 AC: 291 AN: 2114

Alfa AF: 0.112 Hom.: 1579

Bravo AF: 0.138

Asia WGS AF: 0.344 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs16969862; hg19: chr15-32994001;