rs17284420

Variant names:

• chr5-83417201-G-C
• rs17284420

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 0.0854 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0855 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

Gnomad4 AFR AF: 0.0528

Gnomad4 AMR AF: 0.0805

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0414

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0974

Gnomad4 OTH AF: 0.0911

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17284420; hg19: chr5-82713020;