rs17284420

chr5-83417201-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;