rs17020634

Variant names:

• chr1-207100612-A-G
• rs17020634

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 0.103 in 152,222 control chromosomes in the GnomAD database, including 985 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 0.10 (985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 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: 0.103 AC: 15683 AN: 152104 Hom.: 985 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.0772

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.103 AC: 15691 AN: 152222 Hom.: 985 Cov.: 32 AF XY: 0.102 AC XY: 7625 AN XY: 74430

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0598

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0834 Hom.: 130

Bravo AF: 0.106

Asia WGS AF: 0.166 AC: 577 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17020634; hg19: chr1-207273957;