chrX-134287375-C-T

Variant names:

• chrX-134287375-C-T
• rs4465121

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 0.176 in 111,203 control chromosomes in the GnomAD database, including 1,533 homozygotes. There are 5,959 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 (1533 hom., 5959 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.176 AC: 19553 AN: 111152 Hom.: 1531 Cov.: 22

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0644

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.0886

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.0979

Gnomad MID AF: 0.0970

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.176 AC: 19587 AN: 111203 Hom.: 1533 Cov.: 22 AF XY: 0.178 AC XY: 5959 AN XY: 33483

African (AFR) AF: 0.228 AC: 6981 AN: 30583

American (AMR) AF: 0.349 AC: 3656 AN: 10481

Ashkenazi Jewish (ASJ) AF: 0.0886 AC: 234 AN: 2641

East Asian (EAS) AF: 0.414 AC: 1445 AN: 3491

South Asian (SAS) AF: 0.303 AC: 799 AN: 2641

European-Finnish (FIN) AF: 0.0979 AC: 581 AN: 5933

Middle Eastern (MID) AF: 0.0926 AC: 20 AN: 216

European-Non Finnish (NFE) AF: 0.105 AC: 5556 AN: 53019

Other (OTH) AF: 0.179 AC: 271 AN: 1515

Alfa AF: 0.135 Hom.: 2606

Bravo AF: 0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.57
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4465121; hg19: chrX-133421405;