rs12556591

Variant names:

• chrX-13032507-A-G
• rs12556591

Your query was ambiguous. Multiple possible variants found:

• chrX-13032507-A-G
• chrX-13032507-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 0.441 in 110,256 control chromosomes in the GnomAD database, including 8,179 homozygotes. There are 14,665 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 0.44 (8179 hom., 14665 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.621 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: 0.441 AC: 48606 AN: 110204 Hom.: 8175 Cov.: 22

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.441 AC: 48615 AN: 110256 Hom.: 8179 Cov.: 22 AF XY: 0.451 AC XY: 14665 AN XY: 32544

African (AFR) AF: 0.243 AC: 7378 AN: 30411

American (AMR) AF: 0.634 AC: 6551 AN: 10332

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1212 AN: 2626

East Asian (EAS) AF: 0.631 AC: 2203 AN: 3490

South Asian (SAS) AF: 0.623 AC: 1609 AN: 2583

European-Finnish (FIN) AF: 0.570 AC: 3272 AN: 5741

Middle Eastern (MID) AF: 0.469 AC: 100 AN: 213

European-Non Finnish (NFE) AF: 0.481 AC: 25356 AN: 52674

Other (OTH) AF: 0.458 AC: 692 AN: 1511

Alfa AF: 0.472 Hom.: 50519

Bravo AF: 0.447

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.70
DANN	Benign	0.52
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12556591; hg19: chrX-13050626;