rs3732410
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001366282.2(GOLGB1):āc.3650A>Gā(p.Tyr1217Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 1,613,820 control chromosomes in the GnomAD database, including 44,756 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: š 0.20 ( 3651 hom., cov: 32)
Exomes š: 0.23 ( 41105 hom. )
Consequence
GOLGB1
NM_001366282.2 missense
NM_001366282.2 missense
Scores
8
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.95
Genes affected
GOLGB1 (HGNC:4429): (golgin B1) Enables RNA binding activity. Involved in protein localization to pericentriolar material. Located in Golgi apparatus and endoplasmic reticulum-Golgi intermediate compartment. [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 (MetaRNN=0.002850145).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGB1 | NM_001366282.2 | c.3650A>G | p.Tyr1217Cys | missense_variant | 13/22 | ENST00000614479.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGB1 | ENST00000614479.5 | c.3650A>G | p.Tyr1217Cys | missense_variant | 13/22 | 1 | NM_001366282.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.199 AC: 30212AN: 152080Hom.: 3652 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.231 AC: 58132AN: 251292Hom.: 7800 AF XY: 0.237 AC XY: 32174AN XY: 135808
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GnomAD4 exome AF: 0.231 AC: 337776AN: 1461620Hom.: 41105 Cov.: 36 AF XY: 0.232 AC XY: 168557AN XY: 727138
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GnomAD4 genome ? AF: 0.199 AC: 30216AN: 152200Hom.: 3651 Cov.: 32 AF XY: 0.198 AC XY: 14711AN XY: 74416
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830
ALSPAC
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861
ESP6500AA
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327
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ExAC
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28046
Asia WGS
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993
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3478
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T;T;T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.;.
MutationTaster
Benign
P;P
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;.;D
REVEL
Benign
Sift
Benign
T;T;.;T
Sift4G
Uncertain
D;D;D;.
Polyphen
D;.;.;P
Vest4
MPC
0.18
ClinPred
T
GERP RS
Varity_R
gMVP
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