X-133527827-A-G

Position:

• chrX-133527827-A-G

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 0.22 in 109,021 control chromosomes in the GnomAD database, including 3,067 homozygotes. There are 6,410 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 0.22 (3067 hom., 6410 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.220 AC: 23948 AN: 108975 Hom.: 3059 Cov.: 21 AF XY: 0.203 AC XY: 6399 AN XY: 31467

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.220 AC: 23974 AN: 109021 Hom.: 3067 Cov.: 21 AF XY: 0.203 AC XY: 6410 AN XY: 31523

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.0757

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.216

Alfa AF: 0.161 Hom.: 2876

Bravo AF: 0.241

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	11
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957030; hg19: chrX-132661855;