rs707254

chrX-131612836-A-GchrX-131612836-A-T

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 0.324 in 110,365 control chromosomes in the GnomAD database, including 4,584 homozygotes. There are 10,514 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 0.32 (4584 hom., 10514 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 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: 0.324 AC: 35789 AN: 110311 Hom.: 4582 Cov.: 22 AF XY: 0.323 AC XY: 10505 AN XY: 32571

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.324 AC: 35796 AN: 110365 Hom.: 4584 Cov.: 22 AF XY: 0.322 AC XY: 10514 AN XY: 32635

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.344

Alfa AF: 0.362 Hom.: 8771

Bravo AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.4

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs707254; hg19: chrX-130746838;