rs10504106

Positions:

• chr8-50395966-G-A

Variant summary

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

The NM_018967.5(SNTG1):​c.27+1701G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,190 control chromosomes in the GnomAD database, including 4,333 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 0.23 (4333 hom., cov: 31)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

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]

SNTG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNTG1	NM_018967.5	c.27+1701G>A		intron_variant		ENST00000642720.2	NP_061840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNTG1	ENST00000642720.2	c.27+1701G>A		intron_variant			NM_018967.5	ENSP00000493900.1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34298 AN: 152072 Hom.: 4322 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0638

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.226 AC: 34326 AN: 152190 Hom.: 4333 Cov.: 31 AF XY: 0.220 AC XY: 16360 AN XY: 74406

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0637

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.240

Alfa AF: 0.256 Hom.: 876

Bravo AF: 0.223

Asia WGS AF: 0.183 AC: 637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.068
DANN	Benign	0.20

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: rs10504106; hg19: chr8-51308526;