rs1373592

Positions:

• chrX-25761468-T-C

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 0.401 in 110,908 control chromosomes in the GnomAD database, including 6,555 homozygotes. There are 13,079 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 0.40 (6555 hom., 13079 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 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: 0.401 AC: 44451 AN: 110856 Hom.: 6558 Cov.: 23 AF XY: 0.395 AC XY: 13061 AN XY: 33100

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.401 AC: 44461 AN: 110908 Hom.: 6555 Cov.: 23 AF XY: 0.394 AC XY: 13079 AN XY: 33162

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.376

Alfa AF: 0.436 Hom.: 3398

Bravo AF: 0.396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373592; hg19: chrX-25779585;