8-50402317-T-G
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018967.5(SNTG1):āc.135T>Gā(p.Cys45Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,609,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000072 ( 0 hom., cov: 32)
Exomes š: 0.00015 ( 0 hom. )
Consequence
SNTG1
NM_018967.5 missense
NM_018967.5 missense
Scores
4
10
5
Clinical Significance
Conservation
PhyloP100: 1.21
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 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.777
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNTG1 | NM_018967.5 | c.135T>G | p.Cys45Trp | missense_variant | 4/19 | ENST00000642720.2 | NP_061840.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNTG1 | ENST00000642720.2 | c.135T>G | p.Cys45Trp | missense_variant | 4/19 | NM_018967.5 | ENSP00000493900 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152212Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000366 AC: 9AN: 245588Hom.: 0 AF XY: 0.0000302 AC XY: 4AN XY: 132598
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GnomAD4 exome AF: 0.000152 AC: 222AN: 1457646Hom.: 0 Cov.: 33 AF XY: 0.000143 AC XY: 104AN XY: 724928
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GnomAD4 genome AF: 0.0000723 AC: 11AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74376
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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 | Jan 06, 2023 | The c.135T>G (p.C45W) alteration is located in exon 4 (coding exon 2) of the SNTG1 gene. This alteration results from a T to G substitution at nucleotide position 135, causing the cysteine (C) at amino acid position 45 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;.;.;T;.;.;.;.;.;.;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.;.;M;.;.;M;.;.;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;.;.;.;D;.;.;D;.;D;.;.
REVEL
Uncertain
Sift
Uncertain
D;.;.;.;D;.;.;D;.;D;.;.
Sift4G
Uncertain
D;.;.;.;D;.;.;D;.;D;.;.
Polyphen
D;D;.;.;D;.;.;D;.;.;.;.
Vest4
MVP
MPC
0.40
ClinPred
D
GERP RS
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