8-50500031-C-T

Variant names:

• chr8-50500031-C-T
• rs310558
• NM_018967.5:c.364-2747C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018967.5(SNTG1):​c.364-2747C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,782 control chromosomes in the GnomAD database, including 41,470 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 0.72 (41470 hom., cov: 31)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 10 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018967.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTG1	NM_018967.5	MANE Select	c.364-2747C>T		intron	N/A	NP_061840.1
	SNTG1	NM_001287813.3		c.364-2747C>T		intron	N/A	NP_001274742.1
	SNTG1	NM_001321773.2		c.364-2747C>T		intron	N/A	NP_001308702.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTG1	ENST00000642720.2	MANE Select	c.364-2747C>T		intron	N/A	ENSP00000493900.1
	SNTG1	ENST00000518864.5	TSL:1	c.364-2747C>T		intron	N/A	ENSP00000429276.1
	SNTG1	ENST00000517473.5	TSL:1	c.364-2747C>T		intron	N/A	ENSP00000431123.1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 109961 AN: 151664 Hom.: 41462 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.725 AC: 110018 AN: 151782 Hom.: 41470 Cov.: 31 AF XY: 0.723 AC XY: 53661 AN XY: 74186

African (AFR) AF: 0.498 AC: 20587 AN: 41374

American (AMR) AF: 0.758 AC: 11561 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2759 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4352 AN: 5148

South Asian (SAS) AF: 0.753 AC: 3630 AN: 4820

European-Finnish (FIN) AF: 0.786 AC: 8292 AN: 10544

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.830 AC: 56293 AN: 67854

Other (OTH) AF: 0.741 AC: 1563 AN: 2110

Alfa AF: 0.788 Hom.: 94133

Bravo AF: 0.714

Asia WGS AF: 0.782 AC: 2700 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		-0.41
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: rs310558; hg19: chr8-51412591;