rs11211670

Positions:

• chr2-1363263-G-C
• chr2-1363263-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018968.4(SNTG2):​c.1489-4080G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,056 control chromosomes in the GnomAD database, including 5,824 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 0.27 (5824 hom., cov: 32)
• Consequence: SNTG2 NM_018968.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

SNTG2 (HGNC:13741): (syntrophin gamma 2) This gene encodes a protein belonging to the syntrophin family. Syntrophins are cytoplasmic peripheral membrane proteins that bind to components of mechanosenstive sodium channels and the extreme carboxy-terminal domain of dystrophin and dystrophin-related proteins. The PDZ domain of this protein product interacts with a protein component of a mechanosensitive sodium channel that affects channel gating. Absence or reduction of this protein product has been associated with Duchenne muscular dystrophy. There is evidence of alternative splicing yet the full-length nature of these variants has not been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNTG2	NM_018968.4	c.1489-4080G>C		intron_variant		ENST00000308624.10	NP_061841.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNTG2	ENST00000308624.10	c.1489-4080G>C		intron_variant		1	NM_018968.4	ENSP00000311837	P1
SNTG2	ENST00000407292.1	c.1108-4080G>C		intron_variant		1		ENSP00000385020
SNTG2	ENST00000471239.1	n.518-4080G>C		intron_variant, non_coding_transcript_variant		3
SNTG2	ENST00000472606.1	n.178-4080G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40709 AN: 151938 Hom.: 5812 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.268 AC: 40744 AN: 152056 Hom.: 5824 Cov.: 32 AF XY: 0.270 AC XY: 20105 AN XY: 74330

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.285

Alfa AF: 0.258 Hom.: 659

Bravo AF: 0.267

Asia WGS AF: 0.402 AC: 1394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.28

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: rs11211670; hg19: chr2-1367035;