8-50450688-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_018967.5(SNTG1):c.322A>T(p.Ile108Leu) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SNTG1 NM_018967.5 missense, splice_region
• Scores: Splicing: ADA: 0.008691
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.14

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNTG1	NM_018967.5	c.322A>T	p.Ile108Leu	missense_variant, splice_region_variant	8/19	ENST00000642720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNTG1	ENST00000642720.2	c.322A>T	p.Ile108Leu	missense_variant, splice_region_variant	8/19		NM_018967.5	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 15, 2023

The c.322A>T (p.I108L) alteration is located in exon 8 (coding exon 6) of the SNTG1 gene. This alteration results from a A to T substitution at nucleotide position 322, causing the isoleucine (I) at amino acid position 108 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.88
BayesDel_addAF	Benign	-0.042	T
BayesDel_noAF	Benign	-0.30
Cadd	Pathogenic	27
Dann	Uncertain	0.99
DEOGEN2	Benign	0.040	T;T;.;.;.;T;.;.;.;.;.
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Uncertain	0.95	D
M_CAP	Benign	0.0076	T
MetaRNN	Uncertain	0.55	D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	1.9	L;L;.;.;.;L;.;L;.;.;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.90	D
PROVEAN	Benign	-1.8	N;.;.;.;.;N;.;N;.;.;.
REVEL	Benign	0.17
Sift	Uncertain	0.0060	D;.;.;.;.;D;.;D;.;.;.
Sift4G	Uncertain	0.011	D;.;.;.;.;D;.;D;.;.;.
Polyphen		0.70	P;P;.;.;.;P;.;P;.;.;.
Vest4		0.79
MutPred		0.66		Loss of catalytic residue at I108 (P = 0.0483);Loss of catalytic residue at I108 (P = 0.0483);.;Loss of catalytic residue at I108 (P = 0.0483);.;Loss of catalytic residue at I108 (P = 0.0483);Loss of catalytic residue at I108 (P = 0.0483);Loss of catalytic residue at I108 (P = 0.0483);Loss of catalytic residue at I108 (P = 0.0483);Loss of catalytic residue at I108 (P = 0.0483);Loss of catalytic residue at I108 (P = 0.0483);
MVP		0.39
MPC		0.16
ClinPred		0.95	D
GERP RS		4.4
Varity_R		0.41
gMVP		0.48

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0087
dbscSNV1_RF	Benign	0.21
SpliceAI score (max)		0.15		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-51363248;