X-129866068-A-T

Variant names:

• chrX-129866068-A-T
• rs16999576

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 0.125 in 110,150 control chromosomes in the GnomAD database, including 1,347 homozygotes. There are 3,825 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 0.12 (1347 hom., 3825 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.125 AC: 13754 AN: 110095 Hom.: 1349 Cov.: 21

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0439

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0661

Gnomad MID AF: 0.0586

Gnomad NFE AF: 0.0258

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.125 AC: 13765 AN: 110150 Hom.: 1347 Cov.: 21 AF XY: 0.118 AC XY: 3825 AN XY: 32418

African (AFR) AF: 0.316 AC: 9484 AN: 30053

American (AMR) AF: 0.0554 AC: 568 AN: 10252

Ashkenazi Jewish (ASJ) AF: 0.0439 AC: 116 AN: 2644

East Asian (EAS) AF: 0.310 AC: 1078 AN: 3482

South Asian (SAS) AF: 0.223 AC: 577 AN: 2589

European-Finnish (FIN) AF: 0.0661 AC: 383 AN: 5791

Middle Eastern (MID) AF: 0.0550 AC: 12 AN: 218

European-Non Finnish (NFE) AF: 0.0258 AC: 1366 AN: 52939

Other (OTH) AF: 0.120 AC: 180 AN: 1499

Alfa AF: 0.0766 Hom.: 453

Bravo AF: 0.135

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.61
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs16999576; hg19: chrX-129000044; COSMIC: COSV71312306;