10-86962974-G-C

Variant summary

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

The NM_003087.3(SNCG):ā€‹c.373G>Cā€‹(p.Gly125Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000337 in 1,603,566 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.000026 ( 0 hom., cov: 33)
Exomes š‘“: 0.000034 ( 1 hom. )

Consequence

SNCG
NM_003087.3 missense

Scores

2
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.772
Variant links:
Genes affected
SNCG (HGNC:11141): (synuclein gamma) This gene encodes a member of the synuclein family of proteins which are believed to be involved in the pathogenesis of neurodegenerative diseases. Mutations in this gene have also been associated with breast tumor development. [provided by RefSeq, Jan 2010]
MMRN2 (HGNC:19888): (multimerin 2) This gene encodes a protein belonging to the member of elastin microfibril interface-located (EMILIN) protein family. This family member is an extracellular matrix glycoprotein that can interfere with tumor angiogenesis and growth. It serves as a transforming growth factor beta antagonist and can interfere with the VEGF-A/VEGFR2 pathway. A related pseudogene has been identified on chromosome 6. [provided by RefSeq, Aug 2012]

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=0.105838954).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNCGNM_003087.3 linkc.373G>C p.Gly125Arg missense_variant Exon 5 of 5 ENST00000372017.4 NP_003078.2 O76070Q6FHG5
SNCGXM_047425681.1 linkc.700G>C p.Gly234Arg missense_variant Exon 7 of 7 XP_047281637.1
SNCGNM_001330120.2 linkc.*44G>C 3_prime_UTR_variant Exon 7 of 7 NP_001317049.1 O76070F8W754

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNCGENST00000372017.4 linkc.373G>C p.Gly125Arg missense_variant Exon 5 of 5 1 NM_003087.3 ENSP00000361087.3 O76070

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152214
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000218
AC:
5
AN:
229056
Hom.:
0
AF XY:
0.0000243
AC XY:
3
AN XY:
123446
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000109
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000194
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000345
AC:
50
AN:
1451352
Hom.:
1
Cov.:
31
AF XY:
0.0000375
AC XY:
27
AN XY:
720600
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000464
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000600
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000343
Gnomad4 OTH exome
AF:
0.0000666
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152214
Hom.:
0
Cov.:
33
AF XY:
0.0000403
AC XY:
3
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000264
ExAC
AF:
0.0000165
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.086
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.33
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.055
T
Eigen
Benign
-0.37
Eigen_PC
Benign
-0.32
FATHMM_MKL
Benign
0.62
D
LIST_S2
Benign
0.54
T
M_CAP
Benign
0.029
D
MetaRNN
Benign
0.11
T
MetaSVM
Benign
-0.69
T
MutationAssessor
Uncertain
2.3
M
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-1.2
N
REVEL
Benign
0.21
Sift
Benign
0.042
D
Sift4G
Benign
0.52
T
Polyphen
0.0010
B
Vest4
0.076
MutPred
0.38
Loss of glycosylation at S124 (P = 0.0624);
MVP
0.79
MPC
0.15
ClinPred
0.61
D
GERP RS
0.024
Varity_R
0.049
gMVP
0.30

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: rs374301169; hg19: chr10-88722731; API