X-134932569-C-T

Variant names:

• chrX-134932569-C-T
• rs5930667
• ENST00000842757.1:n.101-128G>A

Variant summary

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

The ENST00000842757.1(ENSG00000309646):​n.101-128G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 110,410 control chromosomes in the GnomAD database, including 4,247 homozygotes. There are 9,949 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 0.31 (4247 hom., 9949 hem., cov: 22)
• Consequence: ENSG00000309646 ENST00000842757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 1 publications found

Genes affected

ENSG00000309646 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842757.1. 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
	ENSG00000309646	ENST00000842757.1		n.101-128G>A		intron	N/A
	ENSG00000309646	ENST00000842758.1		n.194-128G>A		intron	N/A
	ENSG00000309646	ENST00000842759.1		n.210-128G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.311 AC: 34341 AN: 110356 Hom.: 4241 Cov.: 22

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.267

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.311 AC: 34374 AN: 110410 Hom.: 4247 Cov.: 22 AF XY: 0.304 AC XY: 9949 AN XY: 32704

African (AFR) AF: 0.419 AC: 12726 AN: 30345

American (AMR) AF: 0.330 AC: 3415 AN: 10343

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 874 AN: 2634

East Asian (EAS) AF: 0.536 AC: 1833 AN: 3420

South Asian (SAS) AF: 0.358 AC: 934 AN: 2611

European-Finnish (FIN) AF: 0.232 AC: 1364 AN: 5880

Middle Eastern (MID) AF: 0.265 AC: 57 AN: 215

European-Non Finnish (NFE) AF: 0.237 AC: 12512 AN: 52794

Other (OTH) AF: 0.332 AC: 499 AN: 1502

Alfa AF: 0.274 Hom.: 12013

Bravo AF: 0.330

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.6
DANN	Benign	0.86
PhyloP100		0.30

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: rs5930667;

hg19: chrX-134066599;