rs200135028

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001144757.3(SCG5):​c.482G>A​(p.Gly161Asp) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SCG5
NM_001144757.3 missense

Scores

1
4
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.93
Variant links:
Genes affected
SCG5 (HGNC:10816): (secretogranin V) This gene encodes a secreted chaperone protein that prevents the aggregation of other secreted proteins, including proteins that are associated with neurodegenerative and metabolic disease. The encoded protein may be best known for its role in the trafficking and activation of prohormone convertase PC2 (encoded by Gene ID: 5126). Phosphorylation of the encoded protein has been shown to have an inhibitory effect on its chaperone function. This gene also produces a ARHGAP11A-SCG5 readthrough transcript and ARHGAP11A-SCG5 protein. [provided by RefSeq, Feb 2019]
ARHGAP11A-SCG5 (HGNC:56310): (ARHGAP11A-SCG5 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring ARHGAP11A (Rho GTPase activating protein 11A) and SCG5 (secretogranin V) genes on chromosome 15q13.3. The readthrough transcript encodes a fusion protein that shares sequence identity with both the ARHGAP11A and SCG5 gene products. [provided by RefSeq, Feb 2019]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3126297).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCG5NM_001144757.3 linkc.482G>A p.Gly161Asp missense_variant Exon 4 of 6 ENST00000300175.9 NP_001138229.1 P05408-1A0A024R9I1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCG5ENST00000300175.9 linkc.482G>A p.Gly161Asp missense_variant Exon 4 of 6 1 NM_001144757.3 ENSP00000300175.4 P05408-1
ARHGAP11A-SCG5ENST00000692248.1 linkc.1721G>A p.Gly574Asp missense_variant Exon 12 of 14 ENSP00000510771.1 A0A8I5KWH8

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000404
AC:
1
AN:
247582
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
134182
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000559
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1457798
Hom.:
0
Cov.:
28
AF XY:
0.00
AC XY:
0
AN XY:
725312
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
ExAC
AF:
0.00000827
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.28
BayesDel_addAF
Benign
-0.032
T
BayesDel_noAF
Benign
-0.12
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.14
T;.;.;T;T
Eigen
Uncertain
0.36
Eigen_PC
Uncertain
0.46
FATHMM_MKL
Uncertain
0.89
D
M_CAP
Benign
0.0025
T
MetaRNN
Benign
0.31
T;T;T;T;T
MetaSVM
Benign
-0.88
T
MutationAssessor
Benign
1.6
L;.;.;.;.
PrimateAI
Pathogenic
0.82
D
PROVEAN
Benign
0.45
N;N;N;N;N
REVEL
Benign
0.064
Sift
Benign
0.13
T;T;D;D;D
Sift4G
Benign
0.18
T;T;T;T;D
Polyphen
0.67
P;.;.;.;.
Vest4
0.48
MutPred
0.41
Gain of ubiquitination at K166 (P = 0.0388);.;.;Gain of ubiquitination at K166 (P = 0.0388);.;
MVP
0.58
MPC
0.28
ClinPred
0.54
D
GERP RS
5.7
Varity_R
0.14
gMVP
0.47

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: rs200135028; hg19: chr15-32976863; API