rs10504106

Variant names:

• chr8-50395966-G-A
• rs10504106
• NM_018967.5:c.27+1701G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SNTG1	NM_018967.5	c.27+1701G>A		intron_variant	Intron 3 of 18	ENST00000642720.2	NP_061840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNTG1	ENST00000642720.2	c.27+1701G>A		intron_variant	Intron 3 of 18		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

African (AFR) AF: 0.146 AC: 6057 AN: 41510

American (AMR) AF: 0.195 AC: 2981 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3470

East Asian (EAS) AF: 0.0637 AC: 330 AN: 5178

South Asian (SAS) AF: 0.205 AC: 987 AN: 4824

European-Finnish (FIN) AF: 0.203 AC: 2152 AN: 10584

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.298 AC: 20270 AN: 68014

Other (OTH) AF: 0.240 AC: 506 AN: 2112

Alfa AF: 0.254 Hom.: 884

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
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10504106; hg19: chr8-51308526;