chr8-50528144-G-A

Variant names:

• chr8-50528144-G-A
• rs310575
• NM_018967.5:c.467-2033G>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.467-2033G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,522 control chromosomes in the GnomAD database, including 10,108 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 0.34 (10108 hom., cov: 32)
• Consequence: SNTG1 NM_018967.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.542 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.467-2033G>A		intron	N/A	NP_061840.1
	SNTG1	NM_001287813.3		c.467-2033G>A		intron	N/A	NP_001274742.1
	SNTG1	NM_001321773.2		c.467-2033G>A		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.467-2033G>A		intron	N/A	ENSP00000493900.1
	SNTG1	ENST00000518864.5	TSL:1	c.467-2033G>A		intron	N/A	ENSP00000429276.1
	SNTG1	ENST00000517473.5	TSL:1	c.467-2033G>A		intron	N/A	ENSP00000431123.1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51040 AN: 151402 Hom.: 10094 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.337 AC: 51109 AN: 151522 Hom.: 10108 Cov.: 32 AF XY: 0.341 AC XY: 25266 AN XY: 74018

African (AFR) AF: 0.548 AC: 22666 AN: 41362

American (AMR) AF: 0.314 AC: 4782 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3468

East Asian (EAS) AF: 0.233 AC: 1202 AN: 5156

South Asian (SAS) AF: 0.432 AC: 2076 AN: 4810

European-Finnish (FIN) AF: 0.251 AC: 2624 AN: 10448

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.227 AC: 15356 AN: 67732

Other (OTH) AF: 0.331 AC: 697 AN: 2104

Alfa AF: 0.283 Hom.: 903

Bravo AF: 0.347

Asia WGS AF: 0.363 AC: 1261 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.75
PhyloP100		-2.8
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: rs310575; hg19: chr8-51440704;