rs2943134
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001282468.3(GOLGA8M):āc.266G>Cā(p.Arg89Thr) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.000033 ( 0 hom., cov: 20)
Exomes š: 0.000029 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
GOLGA8M
NM_001282468.3 missense
NM_001282468.3 missense
Scores
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.80
Genes affected
GOLGA8M (HGNC:44404): (golgin A8 family member M) Predicted to be involved in Golgi organization. Predicted to be active in Golgi cis cisterna; Golgi cisterna membrane; and cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.11229399).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA8M | NM_001282468.3 | c.266G>C | p.Arg89Thr | missense_variant | 4/19 | ENST00000563027.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA8M | ENST00000563027.2 | c.266G>C | p.Arg89Thr | missense_variant | 4/19 | 5 | NM_001282468.3 | P1 | |
GOLGA8M | ENST00000563213.1 | n.521G>C | non_coding_transcript_exon_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 3AN: 151442Hom.: 0 Cov.: 20 FAILED QC
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?
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GnomAD3 exomes AF: 0.0000148 AC: 1AN: 67582Hom.: 0 AF XY: 0.0000298 AC XY: 1AN XY: 33568
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000286 AC: 41AN: 1432662Hom.: 1 Cov.: 31 AF XY: 0.0000324 AC XY: 23AN XY: 709990
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000330 AC: 5AN: 151556Hom.: 0 Cov.: 20 AF XY: 0.0000540 AC XY: 4AN XY: 74016
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
D;N
PROVEAN
Benign
N
Sift
Benign
T
Sift4G
Benign
T
Vest4
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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