chr1-170532171-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_152281.3(GORAB):​c.-53C>T variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.000000684 in 1,461,092 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

GORAB
NM_152281.3 5_prime_UTR

Scores

1
8
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.40
Variant links:
Genes affected
GORAB (HGNC:25676): (golgin, RAB6 interacting) This gene encodes a member of the golgin family, a group of coiled-coil proteins localized to the Golgi. The encoded protein may function in the secretory pathway. The encoded protein, which also localizes to the cytoplasm, was identified by interactions with the N-terminal kinase-like protein, and thus it may function in mitosis. Mutations in this gene have been associated with geroderma osteodysplastica. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]
GORAB-AS1 (HGNC:54051): (GORAB antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GORABNM_152281.3 linkc.-53C>T 5_prime_UTR_variant Exon 1 of 5 ENST00000367763.8 NP_689494.3 Q5T7V8-1B3KQ87

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GORABENST00000367763 linkc.-53C>T 5_prime_UTR_variant Exon 1 of 5 2 NM_152281.3 ENSP00000356737.4 Q5T7V8-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461092
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
726828
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Uncertain
-0.040
CADD
Benign
20
DANN
Uncertain
1.0
DEOGEN2
Benign
0.029
T;.
Eigen
Benign
-0.019
Eigen_PC
Benign
0.071
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.53
T;T
M_CAP
Uncertain
0.15
D
MetaRNN
Uncertain
0.53
D;D
MetaSVM
Benign
-0.83
T
MutationAssessor
Benign
1.5
L;L
PrimateAI
Uncertain
0.55
T
PROVEAN
Benign
-0.27
N;N
REVEL
Benign
0.29
Sift
Uncertain
0.022
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
0.12
B;P
Vest4
0.56
MutPred
0.32
Loss of disorder (P = 0.0825);Loss of disorder (P = 0.0825);
MVP
0.88
MPC
0.41
ClinPred
0.72
D
GERP RS
5.1
Varity_R
0.098
gMVP
0.11

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.20
Details are displayed if max score is > 0.2
DS_DG_spliceai
0.20
Position offset: -2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-170501312; API