NM_018967.5:c.-27-382T>C

Variant names:

• chr8-50393830-T-C
• rs9298318
• NM_018967.5:c.-27-382T>C

Variant summary

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

The NM_018967.5(SNTG1):​c.-27-382T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 152,180 control chromosomes in the GnomAD database, including 65,421 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 0.92 (65421 hom., cov: 31)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 0 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=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 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.-27-382T>C		intron	N/A	NP_061840.1
	SNTG1	NM_001287813.3		c.-27-382T>C		intron	N/A	NP_001274742.1
	SNTG1	NM_001321773.2		c.-27-382T>C		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.-27-382T>C		intron	N/A	ENSP00000493900.1
	SNTG1	ENST00000518864.5	TSL:1	c.-27-382T>C		intron	N/A	ENSP00000429276.1
	SNTG1	ENST00000517473.5	TSL:1	c.-27-382T>C		intron	N/A	ENSP00000431123.1

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140388 AN: 152062 Hom.: 65397 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.923 AC: 140470 AN: 152180 Hom.: 65421 Cov.: 31 AF XY: 0.920 AC XY: 68474 AN XY: 74398

African (AFR) AF: 0.799 AC: 33142 AN: 41488

American (AMR) AF: 0.898 AC: 13736 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 3370 AN: 3472

East Asian (EAS) AF: 0.904 AC: 4657 AN: 5154

South Asian (SAS) AF: 0.834 AC: 4014 AN: 4814

European-Finnish (FIN) AF: 0.994 AC: 10554 AN: 10614

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67819 AN: 68028

Other (OTH) AF: 0.937 AC: 1981 AN: 2114

Alfa AF: 0.948 Hom.: 9850

Bravo AF: 0.912

Asia WGS AF: 0.864 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	7.1
DANN	Benign	0.66
PhyloP100		-0.11
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: rs9298318; hg19: chr8-51306390;