4-175951769-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000280187.11(GPM6A):c.-23+50540C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,078 control chromosomes in the GnomAD database, including 22,934 homozygotes. 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 0.52 ( 22934 hom., cov: 33)
Consequence
GPM6A
ENST00000280187.11 intron
ENST00000280187.11 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.220
Genes affected
GPM6A (HGNC:4460): (glycoprotein M6A) Predicted to enable calcium channel activity. Involved in neuron migration and stem cell differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC107984113 | XR_001741924.3 | n.437-4071C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPM6A | ENST00000280187.11 | c.-23+50540C>T | intron_variant | 1 | P1 | ||||
GPM6A | ENST00000506894.5 | c.4+50540C>T | intron_variant | 1 | |||||
GPM6A | ENST00000502754.5 | c.-153+20108C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.516 AC: 78470AN: 151960Hom.: 22931 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.516 AC: 78484AN: 152078Hom.: 22934 Cov.: 33 AF XY: 0.518 AC XY: 38535AN XY: 74332
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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