rs1373592

Variant names:

• chrX-25761468-T-C
• rs1373592

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 0.401 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.315 AC: 9641 AN: 30571

American (AMR) AF: 0.362 AC: 3791 AN: 10464

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1167 AN: 2635

East Asian (EAS) AF: 0.282 AC: 977 AN: 3468

South Asian (SAS) AF: 0.307 AC: 821 AN: 2673

European-Finnish (FIN) AF: 0.460 AC: 2710 AN: 5885

Middle Eastern (MID) AF: 0.419 AC: 88 AN: 210

European-Non Finnish (NFE) AF: 0.461 AC: 24369 AN: 52815

Other (OTH) AF: 0.376 AC: 569 AN: 1515

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1373592; hg19: chrX-25779585;