rs17002122

Positions:

• chrX-139449609-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 0.0906 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

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 (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0905 AC: 10123 AN: 111838 Hom.: 404 Cov.: 23 AF XY: 0.0817 AC XY: 2782 AN XY: 34036

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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.0226

Gnomad4 EAS AF: 0.000557

Gnomad4 SAS AF: 0.0141

Gnomad4 FIN AF: 0.0767

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0851 Hom.: 1473

Bravo AF: 0.0915

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17002122; hg19: chrX-138531768;