rs17420782

Variant names:

• chr1-47553550-A-G
• rs17420782

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 0.139 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0860 AC: 3574 AN: 41568

American (AMR) AF: 0.156 AC: 2392 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3472

East Asian (EAS) AF: 0.00404 AC: 21 AN: 5196

South Asian (SAS) AF: 0.160 AC: 773 AN: 4830

European-Finnish (FIN) AF: 0.167 AC: 1767 AN: 10598

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11492 AN: 68024

Other (OTH) AF: 0.164 AC: 347 AN: 2116

Alfa AF: 0.160 Hom.: 3778

Bravo AF: 0.135

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs17420782; hg19: chr1-48019222;