15-49802946-T-A

Variant names:

• chr15-49802946-T-A
• rs16962923

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 0.142 in 152,130 control chromosomes in the GnomAD database, including 1,880 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 (1880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 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: 0.142 AC: 21627 AN: 152012 Hom.: 1874 Cov.: 32

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.142 AC: 21635 AN: 152130 Hom.: 1880 Cov.: 32 AF XY: 0.145 AC XY: 10778 AN XY: 74360

African (AFR) AF: 0.0890 AC: 3697 AN: 41536

American (AMR) AF: 0.168 AC: 2577 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2227 AN: 5148

South Asian (SAS) AF: 0.148 AC: 711 AN: 4812

European-Finnish (FIN) AF: 0.162 AC: 1711 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9835 AN: 67986

Other (OTH) AF: 0.158 AC: 334 AN: 2108

Alfa AF: 0.0827 Hom.: 105

Bravo AF: 0.144

Asia WGS AF: 0.231 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.81
DANN	Benign	0.69
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs16962923; hg19: chr15-50095143;