rs16872251

Variant names:

• chr5-3688474-G-A
• rs16872251

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 0.256 in 151,930 control chromosomes in the GnomAD database, including 5,803 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 0.26 (5803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 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: 0.256 AC: 38809 AN: 151812 Hom.: 5792 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.00753

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.256 AC: 38851 AN: 151930 Hom.: 5803 Cov.: 32 AF XY: 0.249 AC XY: 18525 AN XY: 74254

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.00736

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.266

Alfa AF: 0.227 Hom.: 1983

Bravo AF: 0.267

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.036
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16872251; hg19: chr5-3688588;