chr2-170956457-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015530.5(GORASP2):c.721C>G(p.Pro241Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000558 in 1,611,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000057 ( 0 hom. )
Consequence
GORASP2
NM_015530.5 missense
NM_015530.5 missense
Scores
1
8
10
Clinical Significance
Conservation
PhyloP100: 3.87
Genes affected
GORASP2 (HGNC:17500): (golgi reassembly stacking protein 2) This gene encodes a member of the Golgi reassembly stacking protein family. These proteins may play a role in the stacking of Golgi cisternae and Golgi ribbon formation, as well as Golgi fragmentation during apoptosis or mitosis. The encoded protein also plays a role in the intracellular transport of transforming growth factor alpha and may function as a molecular chaperone. A pseudogene of this gene is located on the short arm of chromosome 2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.072993815).
BS2
?
High AC in GnomAd at 7 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GORASP2 | NM_015530.5 | c.721C>G | p.Pro241Ala | missense_variant | 7/10 | ENST00000234160.5 | |
GORASP2 | NM_001201428.2 | c.517C>G | p.Pro173Ala | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GORASP2 | ENST00000234160.5 | c.721C>G | p.Pro241Ala | missense_variant | 7/10 | 1 | NM_015530.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000461 AC: 7AN: 151788Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000144 AC: 36AN: 250466Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135388
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GnomAD4 exome AF: 0.0000569 AC: 83AN: 1459894Hom.: 0 Cov.: 29 AF XY: 0.0000578 AC XY: 42AN XY: 726400
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GnomAD4 genome ? AF: 0.0000461 AC: 7AN: 151906Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74218
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2021 | The c.721C>G (p.P241A) alteration is located in exon 7 (coding exon 7) of the GORASP2 gene. This alteration results from a C to G substitution at nucleotide position 721, causing the proline (P) at amino acid position 241 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
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
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
T
Polyphen
B
Vest4
MutPred
Loss of sheet (P = 0.0104);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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