chrX-13785841-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001001995.3(GPM6B):c.182-33G>A 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 0.60 ( 13958 hom., 19562 hem., cov: 23)
Exomes 𝑓: 0.60 ( 123171 hom. 191233 hem. )
Failed GnomAD Quality Control
Consequence
GPM6B
NM_001001995.3 intron
NM_001001995.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.783
Genes affected
GPM6B (HGNC:4461): (glycoprotein M6B) This gene encodes a membrane glycoprotein that belongs to the proteolipid protein family. Proteolipid protein family members are expressed in most brain regions and are thought to be involved in cellular housekeeping functions such as membrane trafficking and cell-to-cell communication. This protein may also be involved in osteoblast differentiation. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are located on chromosomes Y and 22. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.599 AC: 66027AN: 110261Hom.: 13961 Cov.: 23 AF XY: 0.600 AC XY: 19517AN XY: 32525
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GnomAD3 exomes AF: 0.625 AC: 95747AN: 153076Hom.: 21738 AF XY: 0.632 AC XY: 27163AN XY: 42962
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.598 AC: 611623AN: 1022670Hom.: 123171 Cov.: 19 AF XY: 0.634 AC XY: 191233AN XY: 301412
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.599 AC: 66065AN: 110316Hom.: 13958 Cov.: 23 AF XY: 0.600 AC XY: 19562AN XY: 32590
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Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at