X-134229869-C-T

Variant names:

• chrX-134229869-C-T
• rs7059861

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 0.18 in 109,095 control chromosomes in the GnomAD database, including 1,717 homozygotes. There are 5,354 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 0.18 (1717 hom., 5354 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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: 0.180 AC: 19643 AN: 109054 Hom.: 1717 Cov.: 21

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.0618

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.0948

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.180 AC: 19668 AN: 109095 Hom.: 1717 Cov.: 21 AF XY: 0.170 AC XY: 5354 AN XY: 31541

African (AFR) AF: 0.264 AC: 7931 AN: 30063

American (AMR) AF: 0.339 AC: 3345 AN: 9872

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 189 AN: 2625

East Asian (EAS) AF: 0.404 AC: 1366 AN: 3382

South Asian (SAS) AF: 0.292 AC: 728 AN: 2491

European-Finnish (FIN) AF: 0.0807 AC: 450 AN: 5573

Middle Eastern (MID) AF: 0.0861 AC: 18 AN: 209

European-Non Finnish (NFE) AF: 0.101 AC: 5320 AN: 52705

Other (OTH) AF: 0.187 AC: 279 AN: 1495

Alfa AF: 0.143 Hom.: 14837

Bravo AF: 0.217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7059861;

hg19: chrX-133363899;