rs7890737
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000454189.7(GPM6B):c.4+39672C>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 0.58 ( 14271 hom., 18904 hem., cov: 22)
Failed GnomAD Quality Control
Consequence
GPM6B
ENST00000454189.7 intron
ENST00000454189.7 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.297
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=-0.9).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPM6B | XM_047442007.1 | c.-9872C>T | 5_prime_UTR_variant | 1/8 | |||
GPM6B | NM_001001994.3 | c.4+39672C>T | intron_variant | ||||
GPM6B | NM_001318729.2 | c.4+39672C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPM6B | ENST00000454189.7 | c.4+39672C>T | intron_variant | 1 | A1 | ||||
GPM6B | ENST00000398361.7 | c.-198+39492C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.577 AC: 63654AN: 110251Hom.: 14264 Cov.: 22 AF XY: 0.580 AC XY: 18855AN XY: 32499
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.578 AC: 63710AN: 110301Hom.: 14271 Cov.: 22 AF XY: 0.581 AC XY: 18904AN XY: 32559
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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
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at