X-134251303-C-T

Variant names:

• chrX-134251303-C-T
• rs5975453

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 0.165 in 108,277 control chromosomes in the GnomAD database, including 1,332 homozygotes. There are 5,115 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 0.16 (1332 hom., 5115 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.165 AC: 17814 AN: 108228 Hom.: 1331 Cov.: 21

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0622

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.0819

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.165 AC: 17829 AN: 108277 Hom.: 1332 Cov.: 21 AF XY: 0.167 AC XY: 5115 AN XY: 30697

African (AFR) AF: 0.194 AC: 5788 AN: 29797

American (AMR) AF: 0.352 AC: 3521 AN: 9999

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 185 AN: 2599

East Asian (EAS) AF: 0.423 AC: 1407 AN: 3328

South Asian (SAS) AF: 0.293 AC: 701 AN: 2389

European-Finnish (FIN) AF: 0.0976 AC: 555 AN: 5684

Middle Eastern (MID) AF: 0.0758 AC: 16 AN: 211

European-Non Finnish (NFE) AF: 0.103 AC: 5353 AN: 52130

Other (OTH) AF: 0.178 AC: 261 AN: 1465

Alfa AF: 0.147 Hom.: 4159

Bravo AF: 0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.3
DANN	Benign	0.59
PhyloP100		1.2

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: rs5975453;

hg19: chrX-133385333;