X-129798002-G-T

Variant names:

• chrX-129798002-G-T
• rs760819

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 0.13 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.129 AC: 14383 AN: 111089 Hom.: 1420 Cov.: 22

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

African (AFR) AF: 0.312 AC: 9483 AN: 30420

American (AMR) AF: 0.0812 AC: 858 AN: 10562

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 92 AN: 2634

East Asian (EAS) AF: 0.415 AC: 1429 AN: 3440

South Asian (SAS) AF: 0.170 AC: 458 AN: 2689

European-Finnish (FIN) AF: 0.0568 AC: 342 AN: 6017

Middle Eastern (MID) AF: 0.0512 AC: 11 AN: 215

European-Non Finnish (NFE) AF: 0.0281 AC: 1487 AN: 52963

Other (OTH) AF: 0.135 AC: 206 AN: 1523

Alfa AF: 0.0279 Hom.: 127

Bravo AF: 0.146

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.4
DANN	Benign	0.86
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs760819; hg19: chrX-128931978;