chr5-3688474-G-A

Variant names:

• chr5-3688474-G-A
• rs16872251

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 0.256 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.402 AC: 16656 AN: 41392

American (AMR) AF: 0.210 AC: 3212 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3466

East Asian (EAS) AF: 0.00736 AC: 38 AN: 5166

South Asian (SAS) AF: 0.118 AC: 570 AN: 4818

European-Finnish (FIN) AF: 0.169 AC: 1784 AN: 10550

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14856 AN: 67962

Other (OTH) AF: 0.266 AC: 561 AN: 2110

Alfa AF: 0.229 Hom.: 2244

Bravo AF: 0.267

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.036
DANN	Benign	0.55
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs16872251; hg19: chr5-3688588;