rs5910235

Variant names:

• chrX-117735951-A-G
• rs5910235

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 0.356 in 110,370 control chromosomes in the GnomAD database, including 6,703 homozygotes. There are 11,247 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 0.36 (6703 hom., 11247 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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: 0.356 AC: 39246 AN: 110317 Hom.: 6692 Cov.: 22

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.356 AC: 39311 AN: 110370 Hom.: 6703 Cov.: 22 AF XY: 0.345 AC XY: 11247 AN XY: 32644

African (AFR) AF: 0.660 AC: 19891 AN: 30159

American (AMR) AF: 0.288 AC: 3005 AN: 10435

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 714 AN: 2622

East Asian (EAS) AF: 0.519 AC: 1797 AN: 3465

South Asian (SAS) AF: 0.499 AC: 1287 AN: 2577

European-Finnish (FIN) AF: 0.166 AC: 982 AN: 5916

Middle Eastern (MID) AF: 0.333 AC: 71 AN: 213

European-Non Finnish (NFE) AF: 0.207 AC: 10941 AN: 52808

Other (OTH) AF: 0.346 AC: 518 AN: 1499

Alfa AF: 0.272 Hom.: 31316

Bravo AF: 0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.41
PhyloP100		0.082

Splicing

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

Other links and lift over

dbSNP: rs5910235; hg19: chrX-116869914;