rs17420782

Variant names:

• chr1-47553550-A-G
• rs17420782

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 0.139 in 152,318 control chromosomes in the GnomAD database, including 1,617 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 0.14 (1617 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 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: 0.139 AC: 21160 AN: 152200 Hom.: 1614 Cov.: 33

Gnomad AFR AF: 0.0860

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00422

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.139 AC: 21163 AN: 152318 Hom.: 1617 Cov.: 33 AF XY: 0.138 AC XY: 10279 AN XY: 74472

Gnomad4 AFR AF: 0.0860

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.00404

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.164

Alfa AF: 0.166 Hom.: 2870

Bravo AF: 0.135

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17420782; hg19: chr1-48019222;