rs1911830

Positions:

• chr8-50658612-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• 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]

ACMG classification

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: 84548 AN: 151934 Hom.: 25755 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.570

GnomAD3 exomes AF: 0.612 AC: 151532 AN: 247602 Hom.: 48268 AF XY: 0.616 AC XY: 82502 AN XY: 133938

Gnomad AFR exome AF: 0.281

Gnomad AMR exome AF: 0.558

Gnomad ASJ exome AF: 0.645

Gnomad EAS exome AF: 0.657

Gnomad SAS exome AF: 0.474

Gnomad FIN exome AF: 0.713

Gnomad NFE exome AF: 0.682

Gnomad OTH exome AF: 0.634

GnomAD4 exome AF: 0.658 AC: 954660 AN: 1451814 Hom.: 319325 Cov.: 31 AF XY: 0.654 AC XY: 472476 AN XY: 722636

Gnomad4 AFR exome AF: 0.274

Gnomad4 AMR exome AF: 0.564

Gnomad4 ASJ exome AF: 0.645

Gnomad4 EAS exome AF: 0.669

Gnomad4 SAS exome AF: 0.480

Gnomad4 FIN exome AF: 0.710

Gnomad4 NFE exome AF: 0.686

Gnomad4 OTH exome AF: 0.630

GnomAD4 genome AF: 0.556 AC: 84538 AN: 152052 Hom.: 25751 Cov.: 32 AF XY: 0.558 AC XY: 41439 AN XY: 74316

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.566

Alfa AF: 0.620 Hom.: 22724

Bravo AF: 0.536

Asia WGS AF: 0.514 AC: 1785 AN: 3476

EpiCase AF: 0.671

EpiControl AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.0
DANN	Benign	0.67

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: rs1911830; hg19: chr8-51571172; COSMIC: COSV52471518;