rs12556591

Positions:

• chrX-13032507-A-G
• chrX-13032507-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 0.441 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.441 AC: 48606 AN: 110204 Hom.: 8175 Cov.: 22 AF XY: 0.451 AC XY: 14654 AN XY: 32482

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.458

Alfa AF: 0.488 Hom.: 37907

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12556591; hg19: chrX-13050626;