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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.205 AC: 6299 AN: 30776

American (AMR) AF: 0.385 AC: 4042 AN: 10496

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1205 AN: 2624

East Asian (EAS) AF: 0.497 AC: 1739 AN: 3502

South Asian (SAS) AF: 0.235 AC: 629 AN: 2672

European-Finnish (FIN) AF: 0.219 AC: 1284 AN: 5869

Middle Eastern (MID) AF: 0.290 AC: 62 AN: 214

European-Non Finnish (NFE) AF: 0.338 AC: 17849 AN: 52855

Other (OTH) AF: 0.328 AC: 495 AN: 1510

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1390534; hg19: chrX-78847548;