dbSNP rs4351800: SYT9:c.*1788A>C (chr11-7468588-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_175733.4(SYT9):c.*1788A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 340,782 control chromosomes in the GnomAD database, including 58,956 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 0.60 ( 27718 hom., cov: 33)

Exomes 𝑓: 0.57 ( 31238 hom. )

Consequence

SYT9
NM_175733.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Publications

13 publications found

Variant links:

Genes affected

SYT9 (HGNC:19265): (synaptotagmin 9) Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and syntaxin binding activity. Predicted to be involved in calcium-ion regulated exocytosis; cellular response to calcium ion; and regulation of secretion by cell. Predicted to be located in clathrin-coated endocytic vesicle membrane. Predicted to be active in hippocampal mossy fiber to CA3 synapse; plasma membrane; and secretory vesicle. Predicted to be integral component of synaptic vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]

SYT9 links:

SYT9-AS1 (HGNC:56173): (SYT9 antisense RNA 1)

SYT9-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SYT9	NM_175733.4 link	c.*1788A>C	3_prime_UTR_variant	Exon 7 of 7	ENST00000318881.11	NP_783860.1	Q86SS6
SYT9	XM_011519901.3 link	c.*1720A>C	3_prime_UTR_variant	Exon 8 of 8		XP_011518203.1
SYT9	XM_047426379.1 link	c.*1788A>C	3_prime_UTR_variant	Exon 7 of 7		XP_047282335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYT9	ENST00000318881.11 link	c.*1788A>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_175733.4	ENSP00000324419.6		Q86SS6

Frequencies

GnomAD3 genomes

AF:

0.599

AC:

91055

AN:

152004

Hom.:

27673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.647

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.625

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.327

Gnomad SAS

AF:

0.569

Gnomad FIN

AF:

0.628

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.591

Gnomad OTH

AF:

0.580

GnomAD4 exome

AF:

0.570

AC:

107541

AN:

188658

Hom.:

31238

Cov.:

AF XY:

0.570

AC XY:

54545

AN XY:

95768

show subpopulations

African (AFR)

AF:

0.639

AC:

3696

AN:

5780

American (AMR)

AF:

0.644

AC:

3640

AN:

5650

Ashkenazi Jewish (ASJ)

AF:

0.489

AC:

3543

AN:

7240

East Asian (EAS)

AF:

0.346

AC:

5830

AN:

16862

South Asian (SAS)

AF:

0.574

AC:

958

AN:

1670

European-Finnish (FIN)

AF:

0.633

AC:

9695

AN:

15320

Middle Eastern (MID)

AF:

0.534

AC:

536

AN:

1004

European-Non Finnish (NFE)

AF:

0.592

AC:

72415

AN:

122382

Other (OTH)

AF:

0.567

AC:

7228

AN:

12750

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2129

4259

6388

8518

10647

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

270

540

810

1080

1350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.599

AC:

91161

AN:

152124

Hom.:

27718

Cov.:

AF XY:

0.601

AC XY:

44657

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.647

AC:

26866

AN:

41492

American (AMR)

AF:

0.625

AC:

9559

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.482

AC:

1674

AN:

3472

East Asian (EAS)

AF:

0.327

AC:

1690

AN:

5170

South Asian (SAS)

AF:

0.569

AC:

2733

AN:

4806

European-Finnish (FIN)

AF:

0.628

AC:

6649

AN:

10584

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.591

AC:

40169

AN:

67992

Other (OTH)

AF:

0.582

AC:

1229

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1912

3824

5735

7647

9559

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

752

1504

2256

3008

3760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.587

Hom.:

50176

Bravo

AF:

0.599

Asia WGS

AF:

0.480

AC:

1668

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.7

(source)

DANN

Benign

0.65

PhyloP100

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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