Genetic Variant SYT11:c.-42C>T (chr1-155859720-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_152280.5(SYT11):c.-42C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,606,072 control chromosomes in the GnomAD database, including 79,840 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 0.28 ( 6624 hom., cov: 33)

Exomes 𝑓: 0.30 ( 73216 hom. )

Consequence

SYT11
NM_152280.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22

Publications

26 publications found

Variant links:

Genes affected

SYT11 (HGNC:19239): (synaptotagmin 11) This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that are known calcium sensors and mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. The encoded protein is also a substrate for ubiquitin-E3-ligase parkin. The gene has previously been referred to as synaptotagmin XII but has been renamed synaptotagmin XI to be consistent with mouse and rat official nomenclature. [provided by RefSeq, Apr 2010]

SYT11 links:

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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=-0.64).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SYT11	NM_152280.5 link	c.-42C>T	5_prime_UTR_variant	Exon 1 of 4	ENST00000368324.5	NP_689493.3	Q9BT88
SYT11	XM_017000759.3 link	c.-42C>T	5_prime_UTR_variant	Exon 1 of 4		XP_016856248.1
SYT11	XM_005245014.4 link	c.-42C>T	5_prime_UTR_variant	Exon 1 of 4		XP_005245071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYT11	ENST00000368324.5 link	c.-42C>T		5_prime_UTR_variant	Exon 1 of 4	1	NM_152280.5	ENSP00000357307.4		Q9BT88

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42217

AN:

152042

Hom.:

6615

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.195

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.243

Gnomad EAS

AF:

0.702

Gnomad SAS

AF:

0.340

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.287

Gnomad OTH

AF:

0.287

GnomAD2 exomes

AF:

0.337

AC:

84714

AN:

251350

AF XY:

0.331

show subpopulations

Gnomad AFR exome

AF:

0.178

Gnomad AMR exome

AF:

0.455

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.697

Gnomad FIN exome

AF:

0.314

Gnomad NFE exome

AF:

0.278

Gnomad OTH exome

AF:

0.311

GnomAD4 exome

AF:

0.304

AC:

442614

AN:

1453912

Hom.:

73216

Cov.:

AF XY:

0.304

AC XY:

219854

AN XY:

723818

show subpopulations

African (AFR)

AF:

0.176

AC:

5847

AN:

33310

American (AMR)

AF:

0.442

AC:

19745

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

6553

AN:

26076

East Asian (EAS)

AF:

0.743

AC:

29452

AN:

39664

South Asian (SAS)

AF:

0.333

AC:

28656

AN:

86078

European-Finnish (FIN)

AF:

0.307

AC:

16361

AN:

53356

Middle Eastern (MID)

AF:

0.209

AC:

1198

AN:

5742

European-Non Finnish (NFE)

AF:

0.287

AC:

316601

AN:

1104852

Other (OTH)

AF:

0.303

AC:

18201

AN:

60130

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

15137

30274

45411

60548

75685

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10804

21608

32412

43216

54020

<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:

0.278

AC:

42243

AN:

152160

Hom.:

6624

Cov.:

AF XY:

0.282

AC XY:

20977

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.181

AC:

7512

AN:

41534

American (AMR)

AF:

0.324

AC:

4964

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.243

AC:

842

AN:

3470

East Asian (EAS)

AF:

0.702

AC:

3624

AN:

5162

South Asian (SAS)

AF:

0.339

AC:

1637

AN:

4824

European-Finnish (FIN)

AF:

0.313

AC:

3309

AN:

10576

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.287

AC:

19508

AN:

67976

Other (OTH)

AF:

0.284

AC:

602

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1503

3006

4509

6012

7515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<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:

0.281

Hom.:

8305

Bravo

AF:

0.280

Asia WGS

AF:

0.508

AC:

1766

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

1.2

PromoterAI

-0.071

Neutral

(source)

Mutation Taster

=298/2

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