16-1151615-G-A

Position:

• chr16-1151615-G-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 0.136 in 152,262 control chromosomes in the GnomAD database, including 1,848 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 (1848 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 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: 0.136 AC: 20735 AN: 152144 Hom.: 1847 Cov.: 33

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.136 AC: 20736 AN: 152262 Hom.: 1848 Cov.: 33 AF XY: 0.131 AC XY: 9788 AN XY: 74440

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.152

Alfa AF: 0.139 Hom.: 679

Bravo AF: 0.130

Asia WGS AF: 0.0700 AC: 243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809635; hg19: chr16-1201615;