X-134188574-C-T

Variant names:

• chrX-134188574-C-T
• rs765132
• ENST00000849465.1:n.377C>T

Variant summary

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

The ENST00000849465.1(ENSG00000310384):​n.377C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 110,899 control chromosomes in the GnomAD database, including 353 homozygotes. There are 2,076 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 0.061 (353 hom., 2076 hem., cov: 22)
• Consequence: ENSG00000310384 ENST00000849465.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 3 publications found

Genes affected

ENSG00000310384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849465.1. 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
	ENSG00000310384	ENST00000849465.1		n.377C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0610 AC: 6764 AN: 110861 Hom.: 351 Cov.: 22

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0575

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0251

Gnomad NFE AF: 0.0553

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0611 AC: 6771 AN: 110899 Hom.: 353 Cov.: 22 AF XY: 0.0627 AC XY: 2076 AN XY: 33105

African (AFR) AF: 0.0126 AC: 386 AN: 30643

American (AMR) AF: 0.271 AC: 2774 AN: 10247

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 125 AN: 2645

East Asian (EAS) AF: 0.00 AC: 0 AN: 3562

South Asian (SAS) AF: 0.0367 AC: 96 AN: 2616

European-Finnish (FIN) AF: 0.0528 AC: 306 AN: 5793

Middle Eastern (MID) AF: 0.0139 AC: 3 AN: 216

European-Non Finnish (NFE) AF: 0.0553 AC: 2932 AN: 52991

Other (OTH) AF: 0.0729 AC: 110 AN: 1508

Alfa AF: 0.0532 Hom.: 1583

Bravo AF: 0.0798

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.7
DANN	Benign	0.65
PhyloP100		-0.011

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: rs765132;

hg19: chrX-133322604;