rs2188457

Variant names:

• chrX-133526341-G-A
• rs2188457

Your query was ambiguous. Multiple possible variants found:

• chrX-133526341-G-A
• chrX-133526341-G-C
• chrX-133526341-G-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 0.279 in 110,688 control chromosomes in the GnomAD database, including 5,418 homozygotes. There are 8,774 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 0.28 (5418 hom., 8774 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 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: 0.279 AC: 30823 AN: 110635 Hom.: 5406 Cov.: 23 AF XY: 0.266 AC XY: 8743 AN XY: 32925

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.279 AC: 30873 AN: 110688 Hom.: 5418 Cov.: 23 AF XY: 0.266 AC XY: 8774 AN XY: 32988

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.263

Alfa AF: 0.140 Hom.: 9274

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2188457; hg19: chrX-132660369;