dbSNP rs1911830: SNTG1:p.Thr329Thr (chr8-50658612-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018967.5(SNTG1):c.987G>A(p.Thr329Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 1,603,866 control chromosomes in the GnomAD database, including 345,076 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 0.56 ( 25751 hom., cov: 32)

Exomes 𝑓: 0.66 ( 319325 hom. )

Consequence

SNTG1
NM_018967.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0870

Variant links:

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]

SNTG1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=0.087 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNTG1	NM_018967.5 link	c.987G>A	p.Thr329Thr	synonymous_variant	Exon 15 of 19	ENST00000642720.2	NP_061840.1	Q9NSN8-1A0A024R7Y0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNTG1	ENST00000642720.2 link	c.987G>A	p.Thr329Thr	synonymous_variant	Exon 15 of 19		NM_018967.5	ENSP00000493900.1		Q9NSN8-1

Frequencies

GnomAD3 genomes

AF:

0.556

AC:

84548

AN:

151934

Hom.:

25755

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.592

Gnomad ASJ

AF:

0.647

Gnomad EAS

AF:

0.665

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.720

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.677

Gnomad OTH

AF:

0.570

GnomAD3 exomes

AF:

0.612

AC:

151532

AN:

247602

Hom.:

48268

AF XY:

0.616

AC XY:

82502

AN XY:

133938

show subpopulations

Gnomad AFR exome

AF:

0.281

Gnomad AMR exome

AF:

0.558

Gnomad ASJ exome

AF:

0.645

Gnomad EAS exome

AF:

0.657

Gnomad SAS exome

AF:

0.474

Gnomad FIN exome

AF:

0.713

Gnomad NFE exome

AF:

0.682

Gnomad OTH exome

AF:

0.634

GnomAD4 exome

AF:

0.658

AC:

954660

AN:

1451814

Hom.:

319325

Cov.:

AF XY:

0.654

AC XY:

472476

AN XY:

722636

show subpopulations

Gnomad4 AFR exome

AF:

0.274

Gnomad4 AMR exome

AF:

0.564

Gnomad4 ASJ exome

AF:

0.645

Gnomad4 EAS exome

AF:

0.669

Gnomad4 SAS exome

AF:

0.480

Gnomad4 FIN exome

AF:

0.710

Gnomad4 NFE exome

AF:

0.686

Gnomad4 OTH exome

AF:

0.630

GnomAD4 genome

AF:

0.556

AC:

84538

AN:

152052

Hom.:

25751

Cov.:

AF XY:

0.558

AC XY:

41439

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.288

Gnomad4 AMR

AF:

0.591

Gnomad4 ASJ

AF:

0.647

Gnomad4 EAS

AF:

0.664

Gnomad4 SAS

AF:

0.468

Gnomad4 FIN

AF:

0.720

Gnomad4 NFE

AF:

0.677

Gnomad4 OTH

AF:

0.566

Alfa

AF:

0.620

Hom.:

22724

Bravo

AF:

0.536

Asia WGS

AF:

0.514

AC:

1785

AN:

3476

EpiCase

AF:

0.671

EpiControl

AF:

0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

5.0

DANN

Benign

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over