rs1373592

Variant names:

• chrX-25761468-T-C
• rs1373592

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;