X-129233560-T-G

Position:

• chrX-129233560-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000653849.1(ENSG00000225689):​n.967-64109A>C variant causes a intron, non coding transcript 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: ENST00000653849.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653849.1	n.967-64109A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.493 AC: 54346 AN: 110208 Hom.: 9808 Cov.: 22 AF XY: 0.484 AC XY: 15742 AN XY: 32500

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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.511

Alfa AF: 0.353 Hom.: 2891

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5932595; hg19: chrX-128367537;