dbSNP rs6455600: SYTL3:c.855+202C>T (chr6-158725839-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_001242394.2(SYTL3):c.855+202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 749,850 control chromosomes in the GnomAD database, including 142,219 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 0.66 ( 34979 hom., cov: 32)

Exomes 𝑓: 0.59 ( 107240 hom. )

Consequence

SYTL3
NM_001242394.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950

Publications

8 publications found

Variant links:

Genes affected

SYTL3 (HGNC:15587): (synaptotagmin like 3) The protein encoded by this gene belongs to a family of peripheral membrane proteins that play a role in vesicular trafficking. This protein binds phospholipids in the presence of calcium ions. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2016]

SYTL3 links:

AMZ2P2 (HGNC:38072): (AMZ2 pseudogene 2)

AMZ2P2 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYTL3	NM_001242394.2 link	c.855+202C>T		intron_variant	Intron 11 of 17	ENST00000611299.5	NP_001229323.1	Q4VX76-1B4E2A9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SYTL3	ENST00000611299.5 link	c.855+202C>T	intron_variant	Intron 11 of 17	5	NM_001242394.2	ENSP00000483936.1	Q4VX76-1
AMZ2P2	ENST00000406819.2 link	n.965G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
SYTL3	ENST00000360448.8 link	c.855+202C>T	intron_variant	Intron 12 of 18	5		ENSP00000353631.4	Q4VX76-1
SYTL3	ENST00000367081.7 link	c.651+202C>T	intron_variant	Intron 9 of 15	5		ENSP00000356048.4	Q4VX76-2

Frequencies

GnomAD3 genomes

AF:

0.659

AC:

100119

AN:

152006

Hom.:

34925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.879

Gnomad AMI

AF:

0.691

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.601

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.665

Gnomad FIN

AF:

0.634

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.637

GnomAD4 exome

AF:

0.586

AC:

350258

AN:

597726

Hom.:

107240

Cov.:

AF XY:

0.591

AC XY:

189074

AN XY:

320028

show subpopulations

African (AFR)

AF:

0.887

AC:

14005

AN:

15794

American (AMR)

AF:

0.429

AC:

13161

AN:

30662

Ashkenazi Jewish (ASJ)

AF:

0.594

AC:

9497

AN:

15984

East Asian (EAS)

AF:

0.159

AC:

5472

AN:

34384

South Asian (SAS)

AF:

0.674

AC:

39057

AN:

57922

European-Finnish (FIN)

AF:

0.637

AC:

28374

AN:

44574

Middle Eastern (MID)

AF:

0.610

AC:

2309

AN:

3788

European-Non Finnish (NFE)

AF:

0.605

AC:

219866

AN:

363636

Other (OTH)

AF:

0.598

AC:

18517

AN:

30982

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

6559

13118

19677

26236

32795

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2130

4260

6390

8520

10650

<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:

0.659

AC:

100223

AN:

152124

Hom.:

34979

Cov.:

AF XY:

0.654

AC XY:

48632

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.880

AC:

36526

AN:

41530

American (AMR)

AF:

0.499

AC:

7622

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.601

AC:

2087

AN:

3472

East Asian (EAS)

AF:

0.187

AC:

965

AN:

5168

South Asian (SAS)

AF:

0.666

AC:

3214

AN:

4824

European-Finnish (FIN)

AF:

0.634

AC:

6698

AN:

10562

Middle Eastern (MID)

AF:

0.568

AC:

167

AN:

294

European-Non Finnish (NFE)

AF:

0.603

AC:

40980

AN:

67982

Other (OTH)

AF:

0.633

AC:

1337

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1611

3222

4832

6443

8054

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<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:

0.611

Hom.:

112145

Bravo

AF:

0.651

Asia WGS

AF:

0.474

AC:

1649

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.5

(source)

DANN

Benign

0.60

PhyloP100

-0.095

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