8-50402258-A-C
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_018967.5(SNTG1):āc.76A>Cā(p.Lys26Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000319 in 1,613,276 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0017 ( 1 hom., cov: 32)
Exomes š: 0.00017 ( 1 hom. )
Consequence
SNTG1
NM_018967.5 missense
NM_018967.5 missense
Scores
5
14
Clinical Significance
Conservation
PhyloP100: 6.53
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 Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0095977485).
BP6
Variant 8-50402258-A-C is Benign according to our data. Variant chr8-50402258-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 728154.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNTG1 | NM_018967.5 | c.76A>C | p.Lys26Gln | 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.76A>C | p.Lys26Gln | missense_variant | 4/19 | NM_018967.5 | ENSP00000493900 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00172 AC: 261AN: 152168Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000459 AC: 115AN: 250530Hom.: 0 AF XY: 0.000295 AC XY: 40AN XY: 135388
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GnomAD4 exome AF: 0.000173 AC: 253AN: 1460990Hom.: 1 Cov.: 33 AF XY: 0.000138 AC XY: 100AN XY: 726774
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GnomAD4 genome AF: 0.00171 AC: 261AN: 152286Hom.: 1 Cov.: 32 AF XY: 0.00173 AC XY: 129AN XY: 74470
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SNTG1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 02, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 21, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.;.;T;.;.;.;.;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.;.;L;.;.;L;.;.;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;.;.;N;.;.;N;.;N;.;.
REVEL
Benign
Sift
Benign
T;.;.;.;T;.;.;T;.;T;.;.
Sift4G
Benign
T;.;.;.;T;.;.;T;.;T;.;.
Polyphen
P;P;.;.;P;.;.;P;.;.;.;.
Vest4
MVP
MPC
0.065
ClinPred
T
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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