rs17002122

Variant names:

• chrX-139449609-A-G
• rs17002122

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 0.0906 in 111,888 control chromosomes in the GnomAD database, including 404 homozygotes. There are 2,796 hemizygotes in GnomAD. 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 0.091 (404 hom., 2796 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.40
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.135 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: 0.0905 AC: 10123 AN: 111838 Hom.: 404 Cov.: 23

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0160

Gnomad AMR AF: 0.0543

Gnomad ASJ AF: 0.0226

Gnomad EAS AF: 0.000555

Gnomad SAS AF: 0.0144

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.0458

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0661

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

GnomAD4 genome AF: 0.0906 AC: 10138 AN: 111888 Hom.: 404 Cov.: 23 AF XY: 0.0820 AC XY: 2796 AN XY: 34096

African (AFR) AF: 0.139 AC: 4277 AN: 30787

American (AMR) AF: 0.0545 AC: 576 AN: 10577

Ashkenazi Jewish (ASJ) AF: 0.0226 AC: 60 AN: 2654

East Asian (EAS) AF: 0.000557 AC: 2 AN: 3590

South Asian (SAS) AF: 0.0141 AC: 38 AN: 2703

European-Finnish (FIN) AF: 0.0767 AC: 462 AN: 6023

Middle Eastern (MID) AF: 0.0548 AC: 12 AN: 219

European-Non Finnish (NFE) AF: 0.0866 AC: 4601 AN: 53132

Other (OTH) AF: 0.0653 AC: 99 AN: 1516

Alfa AF: 0.0846 Hom.: 1634

Bravo AF: 0.0915

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.2
DANN	Benign	0.55
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs17002122; hg19: chrX-138531768;