rs16962871

Variant names:

• chr15-49758627-G-T
• rs16962871

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 0.165 in 151,808 control chromosomes in the GnomAD database, including 2,941 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 0.17 (2941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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: 0.165 AC: 25045 AN: 151686 Hom.: 2930 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0912

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0924

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.165 AC: 25086 AN: 151808 Hom.: 2941 Cov.: 32 AF XY: 0.164 AC XY: 12174 AN XY: 74204

African (AFR) AF: 0.329 AC: 13611 AN: 41404

American (AMR) AF: 0.0820 AC: 1249 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0912 AC: 316 AN: 3466

East Asian (EAS) AF: 0.151 AC: 778 AN: 5150

South Asian (SAS) AF: 0.221 AC: 1065 AN: 4810

European-Finnish (FIN) AF: 0.0924 AC: 977 AN: 10576

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6609 AN: 67856

Other (OTH) AF: 0.141 AC: 297 AN: 2112

Alfa AF: 0.114 Hom.: 2048

Bravo AF: 0.169

Asia WGS AF: 0.241 AC: 838 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.7
DANN	Benign	0.83
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs16962871; hg19: chr15-50050824;