chr8-50768378-A-C

Position:

• chr8-50768378-A-C

Variant summary

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

The NM_018967.5(SNTG1):​c.1395+16267A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,806 control chromosomes in the GnomAD database, including 16,606 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 0.44 (16606 hom., cov: 32)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNTG1	NM_018967.5	c.1395+16267A>C		intron_variant		ENST00000642720.2	NP_061840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNTG1	ENST00000642720.2	c.1395+16267A>C		intron_variant			NM_018967.5	ENSP00000493900.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65952 AN: 151688 Hom.: 16545 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.435 AC: 66078 AN: 151806 Hom.: 16606 Cov.: 32 AF XY: 0.432 AC XY: 32052 AN XY: 74188

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.452

Alfa AF: 0.396 Hom.: 1756

Bravo AF: 0.452

Asia WGS AF: 0.463 AC: 1610 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.57

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: rs4382493; hg19: chr8-51680938;