rs898520

chr8-50176332-A-Gchr8-50176332-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018967.5(SNTG1):c.-28+3697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,018 control chromosomes in the GnomAD database, including 7,184 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 0.30 (7184 hom., cov: 32)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNTG1	NM_018967.5	c.-28+3697A>G		intron_variant		ENST00000642720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNTG1	ENST00000642720.2	c.-28+3697A>G		intron_variant			NM_018967.5	P1

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46252 AN: 151900 Hom.: 7181 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.310

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.305 AC: 46294 AN: 152018 Hom.: 7184 Cov.: 32 AF XY: 0.303 AC XY: 22483 AN XY: 74312

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.307

Alfa AF: 0.299 Hom.: 6570

Bravo AF: 0.308

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.97
Dann	Benign	0.52

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

Other links and lift over

dbSNP: rs898520; hg19: chr8-51088892;