rs926598

Variant names:

• chrX-129861332-C-G
• rs926598

Your query was ambiguous. Multiple possible variants found:

• chrX-129861332-C-G
• chrX-129861332-C-T

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 0.16 in 110,582 control chromosomes in the GnomAD database, including 2,408 homozygotes. There are 4,956 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 0.16 (2408 hom., 4956 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 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: 0.160 AC: 17655 AN: 110534 Hom.: 2409 Cov.: 22

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.0598

Gnomad NFE AF: 0.0260

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.160 AC: 17670 AN: 110582 Hom.: 2408 Cov.: 22 AF XY: 0.151 AC XY: 4956 AN XY: 32888

African (AFR) AF: 0.438 AC: 13199 AN: 30151

American (AMR) AF: 0.0689 AC: 718 AN: 10427

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 120 AN: 2637

East Asian (EAS) AF: 0.315 AC: 1097 AN: 3487

South Asian (SAS) AF: 0.205 AC: 531 AN: 2594

European-Finnish (FIN) AF: 0.0659 AC: 388 AN: 5885

Middle Eastern (MID) AF: 0.0563 AC: 12 AN: 213

European-Non Finnish (NFE) AF: 0.0260 AC: 1376 AN: 52986

Other (OTH) AF: 0.150 AC: 228 AN: 1515

Alfa AF: 0.0997 Hom.: 560

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.76
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs926598; hg19: chrX-128995308;