X-134983524-G-A

Variant names:

• chrX-134983524-G-A
• rs2097402
• ENST00000750476.1:n.234-30190C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000750476.1(ENSG00000297719):​n.234-30190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 111,089 control chromosomes in the GnomAD database, including 5,722 homozygotes. There are 11,793 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 0.37 (5722 hom., 11793 hem., cov: 23)
• Consequence: ENSG00000297719 ENST00000750476.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 0 publications found

Genes affected

ENSG00000297719 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750476.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000297719	ENST00000750476.1		n.234-30190C>T		intron	N/A
	ENSG00000297719	ENST00000750477.1		n.753-30190C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 40678 AN: 111034 Hom.: 5720 Cov.: 23

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.366 AC: 40694 AN: 111089 Hom.: 5722 Cov.: 23 AF XY: 0.354 AC XY: 11793 AN XY: 33325

African (AFR) AF: 0.504 AC: 15373 AN: 30513

American (AMR) AF: 0.276 AC: 2899 AN: 10516

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 926 AN: 2630

East Asian (EAS) AF: 0.457 AC: 1591 AN: 3483

South Asian (SAS) AF: 0.451 AC: 1185 AN: 2630

European-Finnish (FIN) AF: 0.237 AC: 1419 AN: 5978

Middle Eastern (MID) AF: 0.474 AC: 102 AN: 215

European-Non Finnish (NFE) AF: 0.311 AC: 16455 AN: 52935

Other (OTH) AF: 0.377 AC: 571 AN: 1516

Alfa AF: 0.338 Hom.: 38839

Bravo AF: 0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.47
PhyloP100		-0.040

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: rs2097402;

hg19: chrX-134117554;