rs7002235

Variant names:

• chr8-50178708-A-G
• rs7002235
• NM_018967.5:c.-28+6073A>G

Variant summary

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

The NM_018967.5(SNTG1):​c.-28+6073A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,850 control chromosomes in the GnomAD database, including 7,187 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 0.31 (7187 hom., cov: 31)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNTG1	NM_018967.5	c.-28+6073A>G		intron_variant	Intron 2 of 18	ENST00000642720.2	NP_061840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNTG1	ENST00000642720.2	c.-28+6073A>G		intron_variant	Intron 2 of 18		NM_018967.5	ENSP00000493900.1

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46283 AN: 151732 Hom.: 7184 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.305 AC: 46325 AN: 151850 Hom.: 7187 Cov.: 31 AF XY: 0.303 AC XY: 22477 AN XY: 74192

African (AFR) AF: 0.345 AC: 14298 AN: 41396

American (AMR) AF: 0.289 AC: 4406 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3470

East Asian (EAS) AF: 0.153 AC: 786 AN: 5152

South Asian (SAS) AF: 0.427 AC: 2049 AN: 4804

European-Finnish (FIN) AF: 0.234 AC: 2468 AN: 10542

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20285 AN: 67924

Other (OTH) AF: 0.308 AC: 649 AN: 2110

Alfa AF: 0.302 Hom.: 9580

Bravo AF: 0.308

Asia WGS AF: 0.330 AC: 1148 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.34
PhyloP100		-0.89
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: rs7002235; hg19: chr8-51091268;