rs5932755

Variant names:

• chrX-125806388-T-A
• rs5932755

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 0.26 in 108,626 control chromosomes in the GnomAD database, including 2,976 homozygotes. There are 7,760 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 0.26 (2976 hom., 7760 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.260 AC: 28227 AN: 108586 Hom.: 2976 Cov.: 21

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.300

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.260 AC: 28220 AN: 108626 Hom.: 2976 Cov.: 21 AF XY: 0.249 AC XY: 7760 AN XY: 31160

African (AFR) AF: 0.172 AC: 5161 AN: 30045

American (AMR) AF: 0.210 AC: 2110 AN: 10064

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1053 AN: 2612

East Asian (EAS) AF: 0.0432 AC: 150 AN: 3473

South Asian (SAS) AF: 0.135 AC: 338 AN: 2495

European-Finnish (FIN) AF: 0.274 AC: 1496 AN: 5458

Middle Eastern (MID) AF: 0.300 AC: 63 AN: 210

European-Non Finnish (NFE) AF: 0.329 AC: 17169 AN: 52134

Other (OTH) AF: 0.272 AC: 401 AN: 1473

Alfa AF: 0.283 Hom.: 1788

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.028
DANN	Benign	0.30
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs5932755; hg19: chrX-124940370;