X-96302380-T-G

Position:

• chrX-96302380-T-G

Variant summary

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

The ENST00000653599.1(ENSG00000286523):​n.282+69102A>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 0.93 (33210 hom., 29716 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENST00000653599.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653599.1	n.282+69102A>C		intron_variant, non_coding_transcript_variant
	ENST00000669252.1	n.750+57186A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.925 AC: 101492 AN: 109666 Hom.: 33215 Cov.: 22 AF XY: 0.929 AC XY: 29662 AN XY: 31920

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.992

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.917

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: 0.925 AC: 101535 AN: 109716 Hom.: 33210 Cov.: 22 AF XY: 0.929 AC XY: 29716 AN XY: 31980

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.976

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.992

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.917

Alfa AF: 0.938 Hom.: 32564

Bravo AF: 0.925

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1206634; hg19: chrX-95557379;