rs2188457

chrX-133526341-G-AchrX-133526341-G-CchrX-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;