16-15394495-T-A

Position:

• chr16-15394495-T-A

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 0.181 in 152,054 control chromosomes in the GnomAD database, including 2,553 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 0.18 (2553 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.181 AC: 27453 AN: 151938 Hom.: 2549 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.181 AC: 27482 AN: 152054 Hom.: 2553 Cov.: 31 AF XY: 0.179 AC XY: 13285 AN XY: 74326

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.185

Alfa AF: 0.118 Hom.: 220

Bravo AF: 0.174

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs222916; hg19: chr16-15488352;