rs17420782

chr1-47553550-A-G

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/exons	MANE	UniProt

Ensembl

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