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

Variant summary

Our verdict is Benign. The variant received -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

Publications

16 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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

GnomAD2 exomes

AF:

0.612

AC:

151532

AN:

247602

AF XY:

0.616

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 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

African (AFR)

AF:

0.274

AC:

9092

AN:

33186

American (AMR)

AF:

0.564

AC:

24870

AN:

44094

Ashkenazi Jewish (ASJ)

AF:

0.645

AC:

16738

AN:

25940

East Asian (EAS)

AF:

0.669

AC:

26326

AN:

39334

South Asian (SAS)

AF:

0.480

AC:

41031

AN:

85558

European-Finnish (FIN)

AF:

0.710

AC:

37846

AN:

53270

Middle Eastern (MID)

AF:

0.600

AC:

3444

AN:

5742

European-Non Finnish (NFE)

AF:

0.686

AC:

757526

AN:

1104692

Other (OTH)

AF:

0.630

AC:

37787

AN:

59998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.446

Heterozygous variant carriers

14407

28815

43222

57630

72037

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.556

AC:

84538

AN:

152052

Hom.:

25751

Cov.:

AF XY:

0.558

AC XY:

41439

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.288

AC:

11937

AN:

41454

American (AMR)

AF:

0.591

AC:

9017

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.647

AC:

2244

AN:

3470

East Asian (EAS)

AF:

0.664

AC:

3433

AN:

5168

South Asian (SAS)

AF:

0.468

AC:

2256

AN:

4820

European-Finnish (FIN)

AF:

0.720

AC:

7619

AN:

10582

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.677

AC:

46050

AN:

67976

Other (OTH)

AF:

0.566

AC:

1194

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1732

3464

5195

6927

8659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.616

Hom.:

24906

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

(source)

DANN

Benign

0.67

PhyloP100

0.087

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

Splicevardb

1.0

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

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chr8-50658612-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over