X-129798002-G-T

Variant names:

• chrX-129798002-G-T
• rs760819

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 0.13 in 111,144 control chromosomes in the GnomAD database, including 1,420 homozygotes. There are 4,138 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 0.13 (1420 hom., 4138 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 0.129 AC: 14383 AN: 111089 Hom.: 1420 Cov.: 22 AF XY: 0.123 AC XY: 4118 AN XY: 33349

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0514

Gnomad AMR AF: 0.0812

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0568

Gnomad MID AF: 0.0553

Gnomad NFE AF: 0.0281

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.130 AC: 14401 AN: 111144 Hom.: 1420 Cov.: 22 AF XY: 0.124 AC XY: 4138 AN XY: 33414

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.0812

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.0568

Gnomad4 NFE AF: 0.0281

Gnomad4 OTH AF: 0.135

Alfa AF: 0.0279 Hom.: 127

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.4
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs760819; hg19: chrX-128931978;