chr16-15394495-T-A

Variant names:

• chr16-15394495-T-A
• rs222916

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 0.181 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.129 AC: 5369 AN: 41466

American (AMR) AF: 0.151 AC: 2313 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3468

East Asian (EAS) AF: 0.149 AC: 767 AN: 5164

South Asian (SAS) AF: 0.241 AC: 1160 AN: 4816

European-Finnish (FIN) AF: 0.185 AC: 1954 AN: 10586

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14616 AN: 67970

Other (OTH) AF: 0.185 AC: 391 AN: 2108

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
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs222916; hg19: chr16-15488352;