rs247615

Positions:

• chr16-56950851-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;