rs203943

chr8-50066614-C-T

Variant summary

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

The NM_018967.5(SNTG1):c.-102-105947C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 152,214 control chromosomes in the GnomAD database, including 56,981 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 0.86 (56981 hom., cov: 33)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

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 (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNTG1	NM_018967.5	c.-102-105947C>T		intron_variant		ENST00000642720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNTG1	ENST00000642720.2	c.-102-105947C>T		intron_variant			NM_018967.5	P1

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131443 AN: 152096 Hom.: 56932 Cov.: 33

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.864 AC: 131547 AN: 152214 Hom.: 56981 Cov.: 33 AF XY: 0.869 AC XY: 64639 AN XY: 74400

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.843

Alfa AF: 0.869 Hom.: 7118

Bravo AF: 0.861

Asia WGS AF: 0.948 AC: 3294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.3
Dann	Benign	0.68

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: rs203943; hg19: chr8-50979174;