rs16962923

Variant names:

• chr15-49802946-T-A
• rs16962923

Your query was ambiguous. Multiple possible variants found:

• chr15-49802946-T-A
• chr15-49802946-T-C
• chr15-49802946-T-G

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 0.142 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.158

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16962923; hg19: chr15-50095143;