rs1591832

chrX-122265919-A-GchrX-122265919-A-T

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 0.452 in 110,600 control chromosomes in the GnomAD database, including 10,601 homozygotes. There are 14,296 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 0.45 (10601 hom., 14296 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.452 AC: 49956 AN: 110541 Hom.: 10591 Cov.: 22 AF XY: 0.434 AC XY: 14233 AN XY: 32793

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.452 AC: 50031 AN: 110600 Hom.: 10601 Cov.: 22 AF XY: 0.435 AC XY: 14296 AN XY: 32862

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.432

Alfa AF: 0.367 Hom.: 2500

Bravo AF: 0.474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.85
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1591832; hg19: chrX-121399772;