rs1390534

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;