X-133263569-C-G

Variant names:

• chrX-133263569-C-G
• rs5975387

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 0.474 in 107,814 control chromosomes in the GnomAD database, including 11,278 homozygotes. There are 13,547 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 0.47 (11278 hom., 13547 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.474 AC: 51066 AN: 107761 Hom.: 11273 Cov.: 21

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.359

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.474 AC: 51113 AN: 107814 Hom.: 11278 Cov.: 21 AF XY: 0.447 AC XY: 13547 AN XY: 30288

African (AFR) AF: 0.844 AC: 24738 AN: 29315

American (AMR) AF: 0.296 AC: 2949 AN: 9961

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 988 AN: 2589

East Asian (EAS) AF: 0.439 AC: 1484 AN: 3382

South Asian (SAS) AF: 0.479 AC: 1136 AN: 2371

European-Finnish (FIN) AF: 0.281 AC: 1573 AN: 5589

Middle Eastern (MID) AF: 0.355 AC: 75 AN: 211

European-Non Finnish (NFE) AF: 0.329 AC: 17221 AN: 52273

Other (OTH) AF: 0.458 AC: 668 AN: 1458

Alfa AF: 0.199 Hom.: 990

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.025
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs5975387; hg19: chrX-132397597;