rs2499416

Variant names:

• chrX-109954175-G-A
• rs2499416

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;