rs16962871

Positions:

• chr15-49758627-G-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 0.165 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.0820

Gnomad4 ASJ AF: 0.0912

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.0924

Gnomad4 NFE AF: 0.0974

Gnomad4 OTH AF: 0.141

Alfa AF: 0.104 Hom.: 1120

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16962871; hg19: chr15-50050824;