3-168010354-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_014498.5(GOLIM4):​c.2006G>A​(p.Arg669Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,613,284 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 0 hom. )

Consequence

GOLIM4
NM_014498.5 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.270
Variant links:
Genes affected
GOLIM4 (HGNC:15448): (golgi integral membrane protein 4) The Golgi complex plays a key role in the sorting and modification of proteins exported from the endoplasmic reticulum. The protein encoded by this gene is a type II Golgi-resident protein. It may process proteins synthesized in the rough endoplasmic reticulum and assist in the transport of protein cargo through the Golgi apparatus. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08159134).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GOLIM4NM_014498.5 linkc.2006G>A p.Arg669Gln missense_variant Exon 16 of 16 ENST00000470487.6 NP_055313.1 O00461

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GOLIM4ENST00000470487.6 linkc.2006G>A p.Arg669Gln missense_variant Exon 16 of 16 1 NM_014498.5 ENSP00000417354.1 O00461
GOLIM4ENST00000309027.4 linkc.1922G>A p.Arg641Gln missense_variant Exon 15 of 15 1 ENSP00000309893.4 F8W785

Frequencies

GnomAD3 genomes
AF:
0.000191
AC:
29
AN:
152108
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000955
AC:
24
AN:
251300
Hom.:
0
AF XY:
0.0000884
AC XY:
12
AN XY:
135816
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000980
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000158
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000214
AC:
312
AN:
1461058
Hom.:
0
Cov.:
30
AF XY:
0.000215
AC XY:
156
AN XY:
726892
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000259
Gnomad4 OTH exome
AF:
0.000149
GnomAD4 genome
AF:
0.000191
AC:
29
AN:
152226
Hom.:
0
Cov.:
32
AF XY:
0.000188
AC XY:
14
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000294
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000283
Hom.:
0
Bravo
AF:
0.000162
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ExAC
AF:
0.0000906
AC:
11
EpiCase
AF:
0.000327
EpiControl
AF:
0.000119

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Apr 29, 2021
Revvity Omics, Revvity
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.068
BayesDel_addAF
Benign
-0.46
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
15
DANN
Uncertain
1.0
DEOGEN2
Benign
0.010
T;.
Eigen
Benign
-0.39
Eigen_PC
Benign
-0.48
FATHMM_MKL
Benign
0.20
N
LIST_S2
Benign
0.83
T;T
M_CAP
Benign
0.0076
T
MetaRNN
Benign
0.082
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.9
L;.
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.87
N;N
REVEL
Benign
0.057
Sift
Benign
0.076
T;T
Sift4G
Benign
0.31
T;T
Polyphen
0.94
P;P
Vest4
0.058
MVP
0.42
MPC
0.095
ClinPred
0.066
T
GERP RS
2.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.030
gMVP
0.014

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs542482925; hg19: chr3-167728142; API