chr3-37281968-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002078.5(GOLGA4):c.173C>T(p.Thr58Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00291 in 1,611,550 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 53 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 48 hom. )
Consequence
GOLGA4
NM_002078.5 missense
NM_002078.5 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 0.366
Genes affected
GOLGA4 (HGNC:4427): (golgin A4) The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked cisternae (flattened membrane sacs). Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. This gene encodes one of the golgins, a family of proteins localized to the Golgi. This protein has been postulated to play a role in Rab6-regulated membrane-tethering events in the Golgi apparatus. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0015317202).
BP6
Variant 3-37281968-C-T is Benign according to our data. Variant chr3-37281968-C-T is described in ClinVar as [Benign]. Clinvar id is 710917.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0501 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA4 | NM_002078.5 | c.173C>T | p.Thr58Ile | missense_variant | 3/24 | ENST00000361924.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA4 | ENST00000361924.7 | c.173C>T | p.Thr58Ile | missense_variant | 3/24 | 1 | NM_002078.5 |
Frequencies
GnomAD3 genomes AF: 0.0150 AC: 2284AN: 152168Hom.: 52 Cov.: 32
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GnomAD3 exomes AF: 0.00412 AC: 1027AN: 249032Hom.: 26 AF XY: 0.00308 AC XY: 416AN XY: 135008
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GnomAD4 exome AF: 0.00165 AC: 2412AN: 1459264Hom.: 48 Cov.: 31 AF XY: 0.00149 AC XY: 1079AN XY: 725672
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GnomAD4 genome AF: 0.0150 AC: 2284AN: 152286Hom.: 53 Cov.: 32 AF XY: 0.0142 AC XY: 1054AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 30, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;D;N;N;D
REVEL
Benign
Sift
Benign
T;D;T;T;D
Sift4G
Benign
T;T;T;T;D
Polyphen
P;B;.;P;.
Vest4
MVP
MPC
0.053
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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