X-28585448-T-C

Position:

• chrX-28585448-T-C

Variant summary

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

The ENST00000456037.1(ENSG00000223742):​n.88+860A>G 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 0.64 (17047 hom., 19999 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENST00000456037.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000456037.1	n.88+860A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.639 AC: 70217 AN: 109810 Hom.: 17044 Cov.: 22 AF XY: 0.622 AC XY: 19951 AN XY: 32058

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.520

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.612

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: 0.640 AC: 70259 AN: 109861 Hom.: 17047 Cov.: 22 AF XY: 0.623 AC XY: 19999 AN XY: 32119

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.604

Alfa AF: 0.571 Hom.: 17016

Bravo AF: 0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1349846; hg19: chrX-28603565;