X-133527827-A-G

Variant names:

• chrX-133527827-A-G
• rs957030

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 0.22 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• 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 rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.220 AC: 23948 AN: 108975 Hom.: 3059 Cov.: 21

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

African (AFR) AF: 0.434 AC: 12837 AN: 29560

American (AMR) AF: 0.148 AC: 1506 AN: 10208

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 376 AN: 2636

East Asian (EAS) AF: 0.514 AC: 1754 AN: 3413

South Asian (SAS) AF: 0.439 AC: 1064 AN: 2426

European-Finnish (FIN) AF: 0.0757 AC: 434 AN: 5734

Middle Eastern (MID) AF: 0.192 AC: 41 AN: 214

European-Non Finnish (NFE) AF: 0.105 AC: 5531 AN: 52688

Other (OTH) AF: 0.216 AC: 317 AN: 1469

Alfa AF: 0.174 Hom.: 4896

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
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs957030; hg19: chrX-132661855;