rs310575

Positions:

• chr8-50528144-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNTG1	NM_018967.5	c.467-2033G>A		intron_variant		ENST00000642720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNTG1	ENST00000642720.2	c.467-2033G>A		intron_variant			NM_018967.5	P1

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

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.331

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs310575; hg19: chr8-51440704;