rs16962914

Variant names:

• chr15-49801438-T-C
• rs16962914

Your query was ambiguous. Multiple possible variants found:

• chr15-49801438-T-C
• chr15-49801438-T-G

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 0.168 in 152,094 control chromosomes in the GnomAD database, including 2,732 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 (2732 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 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: 0.168 AC: 25476 AN: 151974 Hom.: 2727 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.0712

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.168 AC: 25499 AN: 152094 Hom.: 2732 Cov.: 31 AF XY: 0.163 AC XY: 12104 AN XY: 74364

African (AFR) AF: 0.304 AC: 12590 AN: 41444

American (AMR) AF: 0.113 AC: 1733 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3466

East Asian (EAS) AF: 0.00869 AC: 45 AN: 5178

South Asian (SAS) AF: 0.0714 AC: 345 AN: 4830

European-Finnish (FIN) AF: 0.103 AC: 1094 AN: 10584

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8722 AN: 67988

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.140 Hom.: 4602

Bravo AF: 0.172

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs16962914; hg19: chr15-50093635;