rs1591832

Variant names:

• chrX-122265919-A-G
• rs1591832

Your query was ambiguous. Multiple possible variants found:

• chrX-122265919-A-G
• chrX-122265919-A-T

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 0.452 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.452 AC: 49956 AN: 110541 Hom.: 10591 Cov.: 22

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

African (AFR) AF: 0.844 AC: 25552 AN: 30267

American (AMR) AF: 0.341 AC: 3555 AN: 10419

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 878 AN: 2630

East Asian (EAS) AF: 0.253 AC: 884 AN: 3492

South Asian (SAS) AF: 0.255 AC: 674 AN: 2647

European-Finnish (FIN) AF: 0.314 AC: 1855 AN: 5906

Middle Eastern (MID) AF: 0.411 AC: 88 AN: 214

European-Non Finnish (NFE) AF: 0.299 AC: 15784 AN: 52836

Other (OTH) AF: 0.432 AC: 654 AN: 1514

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1591832; hg19: chrX-121399772;