X-33978185-G-T

Position:

• chrX-33978185-G-T

Variant summary

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

The ENST00000653446.1(ENSG00000233928):​n.287-98281G>T 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 0.79 (24572 hom., 25065 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000233928 ENST00000653446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

ENSG00000233928 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373153	XR_950542.4	n.372-98281G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000233928	ENST00000653446.1	n.287-98281G>T		intron_variant
ENSG00000233928	ENST00000656777.1	n.349-98281G>T		intron_variant
ENSG00000233928	ENST00000656973.1	n.201-98281G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.792 AC: 86646 AN: 109438 Hom.: 24578 Cov.: 22 AF XY: 0.788 AC XY: 25025 AN XY: 31742

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.811

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: 0.792 AC: 86674 AN: 109486 Hom.: 24572 Cov.: 22 AF XY: 0.788 AC XY: 25065 AN XY: 31800

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.806

Alfa AF: 0.787 Hom.: 8583

Bravo AF: 0.800

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3006142; hg19: chrX-33996302;