rs2499416

Variant names:

• chrX-109954175-G-A
• rs2499416

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 0.46 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.460 AC: 50578 AN: 109937 Hom.: 8601 Cov.: 22

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

African (AFR) AF: 0.446 AC: 13522 AN: 30291

American (AMR) AF: 0.316 AC: 3268 AN: 10356

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1120 AN: 2618

East Asian (EAS) AF: 0.225 AC: 779 AN: 3459

South Asian (SAS) AF: 0.348 AC: 887 AN: 2549

European-Finnish (FIN) AF: 0.533 AC: 3028 AN: 5685

Middle Eastern (MID) AF: 0.444 AC: 95 AN: 214

European-Non Finnish (NFE) AF: 0.512 AC: 26947 AN: 52628

Other (OTH) AF: 0.423 AC: 639 AN: 1512

Alfa AF: 0.482 Hom.: 4154

Bravo AF: 0.444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs2499416; hg19: chrX-109197403;