rs247615

Variant names:

• chr16-56950851-A-G
• rs247615

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 0.233 in 151,858 control chromosomes in the GnomAD database, including 4,229 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 0.23 (4229 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 22 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 = 0.255 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: 0.233 AC: 35381 AN: 151740 Hom.: 4218 Cov.: 31

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.233 AC: 35424 AN: 151858 Hom.: 4229 Cov.: 31 AF XY: 0.231 AC XY: 17150 AN XY: 74234

African (AFR) AF: 0.259 AC: 10722 AN: 41392

American (AMR) AF: 0.258 AC: 3925 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3468

East Asian (EAS) AF: 0.107 AC: 550 AN: 5164

South Asian (SAS) AF: 0.247 AC: 1189 AN: 4810

European-Finnish (FIN) AF: 0.171 AC: 1805 AN: 10560

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15650 AN: 67924

Other (OTH) AF: 0.251 AC: 529 AN: 2108

Alfa AF: 0.232 Hom.: 9514

Bravo AF: 0.238

Asia WGS AF: 0.190 AC: 660 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	2.2
DANN	Benign	0.47
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs247615; hg19: chr16-56984763;