rs247615

Variant names:

• chr16-56950851-A-G
• rs247615

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 0.233 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.251

Alfa AF: 0.232 Hom.: 7392

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs247615; hg19: chr16-56984763;