rs16962047

Variant names:

• chr15-49095033-C-T
• rs16962047

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 0.081 in 152,142 control chromosomes in the GnomAD database, including 624 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 0.081 (624 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.0810 AC: 12319 AN: 152024 Hom.: 624 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0566

Gnomad FIN AF: 0.0198

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0810 AC: 12319 AN: 152142 Hom.: 624 Cov.: 32 AF XY: 0.0776 AC XY: 5775 AN XY: 74390

African (AFR) AF: 0.129 AC: 5333 AN: 41500

American (AMR) AF: 0.0802 AC: 1226 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0663 AC: 230 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.0565 AC: 272 AN: 4816

European-Finnish (FIN) AF: 0.0198 AC: 210 AN: 10582

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.0685 AC: 4660 AN: 67986

Other (OTH) AF: 0.100 AC: 212 AN: 2114

Alfa AF: 0.0724 Hom.: 67

Bravo AF: 0.0887

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.73
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs16962047; hg19: chr15-49387230; COSMIC: COSV70609076;