5-83417201-G-C

Variant names:

• chr5-83417201-G-C
• rs17284420

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 0.0854 in 151,748 control chromosomes in the GnomAD database, including 613 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 0.085 (613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.536
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 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: 0.0855 AC: 12962 AN: 151632 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0807

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.0974

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.0854 AC: 12964 AN: 151748 Hom.: 613 Cov.: 32 AF XY: 0.0856 AC XY: 6348 AN XY: 74188

African (AFR) AF: 0.0528 AC: 2186 AN: 41436

American (AMR) AF: 0.0805 AC: 1222 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3464

East Asian (EAS) AF: 0.0414 AC: 213 AN: 5146

South Asian (SAS) AF: 0.123 AC: 590 AN: 4814

European-Finnish (FIN) AF: 0.101 AC: 1060 AN: 10524

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.0974 AC: 6608 AN: 67868

Other (OTH) AF: 0.0911 AC: 192 AN: 2108

Alfa AF: 0.0891 Hom.: 80

Bravo AF: 0.0823

Asia WGS AF: 0.112 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.39
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs17284420; hg19: chr5-82713020;