rs1751725

Variant names:

• chrX-93108601-G-C
• rs1751725

Your query was ambiguous. Multiple possible variants found:

• chrX-93108601-G-C
• chrX-93108601-G-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 0.0796 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0794 AC: 8671 AN: 109172 Hom.: 448 Cov.: 21

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

African (AFR) AF: 0.0402 AC: 1210 AN: 30127

American (AMR) AF: 0.198 AC: 2012 AN: 10165

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 136 AN: 2622

East Asian (EAS) AF: 0.287 AC: 975 AN: 3393

South Asian (SAS) AF: 0.299 AC: 753 AN: 2518

European-Finnish (FIN) AF: 0.0476 AC: 260 AN: 5467

Middle Eastern (MID) AF: 0.0190 AC: 4 AN: 210

European-Non Finnish (NFE) AF: 0.0607 AC: 3191 AN: 52568

Other (OTH) AF: 0.0897 AC: 132 AN: 1472

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
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1751725; hg19: chrX-92363600;