8-50449698-G-C

Variant summary

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

The NM_018967.5(SNTG1):​c.250G>C​(p.Val84Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

SNTG1
NM_018967.5 missense

Scores

1
3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0430
Variant links:
Genes affected
SNTG1 (HGNC:13740): (syntrophin gamma 1) The protein encoded by this gene is a member of the syntrophin family. Syntrophins are cytoplasmic peripheral membrane proteins that typically contain 2 pleckstrin homology (PH) domains, a PDZ domain that bisects the first PH domain, and a C-terminal domain that mediates dystrophin binding. This family member plays a role in mediating gamma-enolase trafficking to the plasma membrane and in enhancing its neurotrophic activity. Mutations in this gene are associated with idiopathic scoliosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2016]

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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=0.17973626).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNTG1NM_018967.5 linkc.250G>C p.Val84Leu missense_variant Exon 6 of 19 ENST00000642720.2 NP_061840.1 Q9NSN8-1A0A024R7Y0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNTG1ENST00000642720.2 linkc.250G>C p.Val84Leu missense_variant Exon 6 of 19 NM_018967.5 ENSP00000493900.1 Q9NSN8-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.59
BayesDel_addAF
Benign
-0.031
T
BayesDel_noAF
Benign
-0.28
CADD
Benign
15
DANN
Benign
0.92
DEOGEN2
Benign
0.075
T;T;.;.;.;T;.;.;.;.;.;.
Eigen
Benign
-0.92
Eigen_PC
Benign
-0.95
FATHMM_MKL
Benign
0.051
N
LIST_S2
Benign
0.83
.;.;T;T;D;T;T;T;T;T;T;T
M_CAP
Benign
0.012
T
MetaRNN
Benign
0.18
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
1.8
L;L;.;.;.;L;.;L;.;.;.;.
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-1.2
N;.;.;.;.;N;.;N;.;N;.;.
REVEL
Benign
0.22
Sift
Uncertain
0.0050
D;.;.;.;.;D;.;D;.;D;.;.
Sift4G
Uncertain
0.0080
D;.;.;.;.;D;.;D;.;D;.;.
Polyphen
0.0060
B;B;.;.;.;B;.;B;.;.;.;.
Vest4
0.65
MutPred
0.61
Gain of catalytic residue at V84 (P = 0.0335);Gain of catalytic residue at V84 (P = 0.0335);.;Gain of catalytic residue at V84 (P = 0.0335);.;Gain of catalytic residue at V84 (P = 0.0335);Gain of catalytic residue at V84 (P = 0.0335);Gain of catalytic residue at V84 (P = 0.0335);Gain of catalytic residue at V84 (P = 0.0335);Gain of catalytic residue at V84 (P = 0.0335);Gain of catalytic residue at V84 (P = 0.0335);Gain of catalytic residue at V84 (P = 0.0335);
MVP
0.60
MPC
0.056
ClinPred
0.58
D
GERP RS
-4.6
Varity_R
0.18
gMVP
0.35

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: rs145093612; hg19: chr8-51362258; API