15-30562188-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP7
The NM_001355476.2(GOLGA8Q):c.1671C>T(p.Pro557Pro) variant causes a synonymous 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. Synonymous variant affecting the same amino acid position (i.e. P557P) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 10)
Exomes 𝑓: 0.000041 ( 14 hom. )
Failed GnomAD Quality Control
Consequence
GOLGA8Q
NM_001355476.2 synonymous
NM_001355476.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.582
Genes affected
GOLGA8Q (HGNC:44408): (golgin A8 family member Q) 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 -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP7
Synonymous conserved (PhyloP=-0.582 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GOLGA8Q | NM_001355476.2 | c.1671C>T | p.Pro557Pro | synonymous_variant | Exon 18 of 19 | ENST00000562783.2 | NP_001342405.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 77918Hom.: 0 Cov.: 10 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000411 AC: 41AN: 998210Hom.: 14 Cov.: 29 AF XY: 0.0000525 AC XY: 26AN XY: 494818
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000257 AC: 2AN: 77918Hom.: 0 Cov.: 10 AF XY: 0.0000266 AC XY: 1AN XY: 37616
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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