rs5910235

Positions:

• chrX-117735951-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;