chrX-117735951-A-G

Variant names:

• chrX-117735951-A-G
• rs5910235

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 0.356 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.356 AC: 39246 AN: 110317 Hom.: 6692 Cov.: 22 AF XY: 0.344 AC XY: 11195 AN XY: 32581

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

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.346

Alfa AF: 0.239 Hom.: 19654

Bravo AF: 0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5910235; hg19: chrX-116869914;