X-129233560-T-G

Variant names:

• chrX-129233560-T-G
• rs5932595
• ENST00000653849.1:n.967-64109A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000653849.1(ENSG00000225689):​n.967-64109A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.49 (9812 hom., 15803 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000225689 ENST00000653849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 1 publications found

Genes affected

ENSG00000225689 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653849.1. 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
	ENSG00000225689	ENST00000653849.1		n.967-64109A>C		intron	N/A
	ENSG00000301792	ENST00000781917.1		n.241+360T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.493 AC: 54346 AN: 110208 Hom.: 9808 Cov.: 22

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.507

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.493 AC: 54412 AN: 110272 Hom.: 9812 Cov.: 22 AF XY: 0.485 AC XY: 15803 AN XY: 32574

African (AFR) AF: 0.586 AC: 17732 AN: 30257

American (AMR) AF: 0.597 AC: 6184 AN: 10367

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1359 AN: 2633

East Asian (EAS) AF: 0.414 AC: 1421 AN: 3434

South Asian (SAS) AF: 0.646 AC: 1665 AN: 2579

European-Finnish (FIN) AF: 0.385 AC: 2253 AN: 5849

Middle Eastern (MID) AF: 0.553 AC: 115 AN: 208

European-Non Finnish (NFE) AF: 0.429 AC: 22629 AN: 52755

Other (OTH) AF: 0.511 AC: 771 AN: 1508

Alfa AF: 0.353 Hom.: 2891

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.74
PhyloP100		0.0070

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: rs5932595;

hg19: chrX-128367537;