rs17622017

Variant names:

• chr1-194372078-C-T
• rs17622017

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 0.0847 in 151,630 control chromosomes in the GnomAD database, including 676 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 (676 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• 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 = 0.112 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: 0.0848 AC: 12844 AN: 151512 Hom.: 676 Cov.: 31

Gnomad AFR AF: 0.0287

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.00772

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0885

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

GnomAD4 genome AF: 0.0847 AC: 12843 AN: 151630 Hom.: 676 Cov.: 31 AF XY: 0.0859 AC XY: 6364 AN XY: 74084

African (AFR) AF: 0.0286 AC: 1185 AN: 41430

American (AMR) AF: 0.0789 AC: 1203 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3468

East Asian (EAS) AF: 0.00793 AC: 41 AN: 5170

South Asian (SAS) AF: 0.109 AC: 520 AN: 4782

European-Finnish (FIN) AF: 0.108 AC: 1133 AN: 10480

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7743 AN: 67754

Other (OTH) AF: 0.0885 AC: 186 AN: 2102

Alfa AF: 0.101 Hom.: 188

Bravo AF: 0.0788

Asia WGS AF: 0.0620 AC: 217 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs17622017; hg19: chr1-194341208;