rs1911830
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_018967.5(SNTG1):c.987G>A(p.Thr329=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 1,603,866 control chromosomes in the GnomAD database, including 345,076 homozygotes. 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: 𝑓 0.56 ( 25751 hom., cov: 32)
Exomes 𝑓: 0.66 ( 319325 hom. )
Consequence
SNTG1
NM_018967.5 synonymous
NM_018967.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0870
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 Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP7
?
Synonymous conserved (PhyloP=0.087 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNTG1 | NM_018967.5 | c.987G>A | p.Thr329= | synonymous_variant | 15/19 | ENST00000642720.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNTG1 | ENST00000642720.2 | c.987G>A | p.Thr329= | synonymous_variant | 15/19 | NM_018967.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.556 AC: 84548AN: 151934Hom.: 25755 Cov.: 32
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GnomAD3 exomes AF: 0.612 AC: 151532AN: 247602Hom.: 48268 AF XY: 0.616 AC XY: 82502AN XY: 133938
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GnomAD4 exome AF: 0.658 AC: 954660AN: 1451814Hom.: 319325 Cov.: 31 AF XY: 0.654 AC XY: 472476AN XY: 722636
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GnomAD4 genome ? AF: 0.556 AC: 84538AN: 152052Hom.: 25751 Cov.: 32 AF XY: 0.558 AC XY: 41439AN XY: 74316
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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