X-33978185-G-T

Variant names:

• chrX-33978185-G-T
• rs3006142
• ENST00000653446.1:n.287-98281G>T

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000233928 (HGNC:):

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653446.1. 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
	ENSG00000233928	ENST00000653446.1		n.287-98281G>T		intron	N/A
	ENSG00000233928	ENST00000656777.1		n.349-98281G>T		intron	N/A
	ENSG00000233928	ENST00000656973.1		n.201-98281G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.792 AC: 86646 AN: 109438 Hom.: 24578 Cov.: 22

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

African (AFR) AF: 0.825 AC: 24751 AN: 30013

American (AMR) AF: 0.821 AC: 8423 AN: 10257

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 2275 AN: 2627

East Asian (EAS) AF: 0.562 AC: 1925 AN: 3424

South Asian (SAS) AF: 0.707 AC: 1787 AN: 2527

European-Finnish (FIN) AF: 0.796 AC: 4559 AN: 5724

Middle Eastern (MID) AF: 0.859 AC: 183 AN: 213

European-Non Finnish (NFE) AF: 0.781 AC: 41020 AN: 52524

Other (OTH) AF: 0.806 AC: 1207 AN: 1498

Alfa AF: 0.787 Hom.: 8583

Bravo AF: 0.800

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.38
PhyloP100		0.33

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: rs3006142;

hg19: chrX-33996302;