rs926598

Positions:

• chrX-129861332-C-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 0.16 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.160 AC: 17655 AN: 110534 Hom.: 2409 Cov.: 22 AF XY: 0.151 AC XY: 4943 AN XY: 32830

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

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.0455

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0260

Gnomad4 OTH AF: 0.150

Alfa AF: 0.0997 Hom.: 560

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926598; hg19: chrX-128995308;