rs4382493

Variant names:

• chr8-50768378-A-C
• rs4382493
• NM_018967.5:c.1395+16267A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-50768378-A-C
• chr8-50768378-A-G
• chr8-50768378-A-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.1395+16267A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,806 control chromosomes in the GnomAD database, including 16,606 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 0.44 (16606 hom., cov: 32)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTG1	NM_018967.5	MANE Select	c.1395+16267A>C		intron	N/A	NP_061840.1
	SNTG1	NM_001287813.3		c.1395+16267A>C		intron	N/A	NP_001274742.1
	SNTG1	NM_001321773.2		c.1395+16267A>C		intron	N/A	NP_001308702.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNTG1	ENST00000642720.2	MANE Select	c.1395+16267A>C		intron	N/A	ENSP00000493900.1
	SNTG1	ENST00000518864.5	TSL:1	c.1395+16267A>C		intron	N/A	ENSP00000429276.1
	SNTG1	ENST00000517473.5	TSL:1	c.1285-24293A>C		intron	N/A	ENSP00000431123.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65952 AN: 151688 Hom.: 16545 Cov.: 32

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.435 AC: 66078 AN: 151806 Hom.: 16606 Cov.: 32 AF XY: 0.432 AC XY: 32052 AN XY: 74188

African (AFR) AF: 0.702 AC: 29070 AN: 41426

American (AMR) AF: 0.364 AC: 5534 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1602 AN: 5116

South Asian (SAS) AF: 0.511 AC: 2465 AN: 4822

European-Finnish (FIN) AF: 0.252 AC: 2665 AN: 10574

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21922 AN: 67868

Other (OTH) AF: 0.452 AC: 952 AN: 2104

Alfa AF: 0.518 Hom.: 5326

Bravo AF: 0.452

Asia WGS AF: 0.463 AC: 1610 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.57
PhyloP100		-0.29
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: rs4382493; hg19: chr8-51680938;