rs1751725

chrX-93108601-G-CchrX-93108601-G-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 0.0796 in 109,217 control chromosomes in the GnomAD database, including 449 homozygotes. There are 2,669 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 0.080 (449 hom., 2669 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 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: 0.0794 AC: 8671 AN: 109172 Hom.: 448 Cov.: 21 AF XY: 0.0837 AC XY: 2654 AN XY: 31702

Gnomad AFR AF: 0.0401

Gnomad AMI AF: 0.0237

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0216

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0853

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

GnomAD4 genome AF: 0.0796 AC: 8689 AN: 109217 Hom.: 449 Cov.: 21 AF XY: 0.0840 AC XY: 2669 AN XY: 31757

Gnomad4 AFR AF: 0.0402

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.0476

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.0897

Alfa AF: 0.0191 Hom.: 91

Bravo AF: 0.0876

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	3.0
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1751725; hg19: chrX-92363600;