rs2499416

chrX-109954175-G-A

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 0.46 in 109,986 control chromosomes in the GnomAD database, including 8,598 homozygotes. There are 14,415 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 0.46 (8598 hom., 14415 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.460 AC: 50578 AN: 109937 Hom.: 8601 Cov.: 22 AF XY: 0.447 AC XY: 14380 AN XY: 32201

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.460 AC: 50608 AN: 109986 Hom.: 8598 Cov.: 22 AF XY: 0.447 AC XY: 14415 AN XY: 32260

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.423

Alfa AF: 0.482 Hom.: 4154

Bravo AF: 0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.0
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2499416; hg19: chrX-109197403;