rs1390534

Variant names:

• chrX-79592051-T-A
• rs1390534

Your query was ambiguous. Multiple possible variants found:

• chrX-79592051-T-A
• chrX-79592051-T-C
• chrX-79592051-T-G

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 0.303 in 111,194 control chromosomes in the GnomAD database, including 3,913 homozygotes. There are 9,862 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 0.30 (3913 hom., 9862 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.303 AC: 33674 AN: 111145 Hom.: 3916 Cov.: 23 AF XY: 0.295 AC XY: 9855 AN XY: 33381

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.302

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.303 AC: 33679 AN: 111194 Hom.: 3913 Cov.: 23 AF XY: 0.295 AC XY: 9862 AN XY: 33440

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.328

Alfa AF: 0.190 Hom.: 960

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.8
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1390534; hg19: chrX-78847548;