Variant rs3744959 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020783.4(SYT4):c.*10C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0978 in 1,609,170 control chromosomes in the GnomAD database, including 11,834 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 0.090 ( 1099 hom., cov: 32)

Exomes 𝑓: 0.099 ( 10735 hom. )

Consequence

SYT4
NM_020783.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.158

Variant links:

Genes affected

SYT4 (HGNC:11512): (synaptotagmin 4) Predicted to enable several functions, including calcium ion binding activity; phospholipid binding activity; and syntaxin binding activity. Involved in negative regulation of catecholamine secretion and positive regulation of dendrite extension. Predicted to be located in several cellular components, including microvesicle; perinuclear region of cytoplasm; and secretory vesicle. Predicted to be active in several cellular components, including axon; exocytic vesicle; and glutamatergic synapse. Predicted to be integral component of neuronal dense core vesicle membrane. [provided by Alliance of Genome Resources, Apr 2022]

SYT4 links:

SYT4 (HGNC:):

SYT4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYT4	NM_020783.4 linkuse as main transcript	c.*10C>T		3_prime_UTR_variant	4/4	ENST00000255224.8	NP_065834.1	Q9H2B2-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SYT4	ENST00000255224 linkuse as main transcript	c.*10C>T	3_prime_UTR_variant	4/4	1	NM_020783.4	ENSP00000255224.2	Q9H2B2-1
SYT4	ENST00000585604.1 linkuse as main transcript	n.596C>T	non_coding_transcript_exon_variant	3/3	1
SYT4	ENST00000590752 linkuse as main transcript	c.*10C>T	3_prime_UTR_variant	4/4	2		ENSP00000466930.1	Q9H2B2-2
SYT4	ENST00000586678.1 linkuse as main transcript	n.478C>T	non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes

AF:

0.0900

AC:

13684

AN:

151976

Hom.:

1092

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0256

Gnomad AMI

AF:

0.0658

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.0288

Gnomad EAS

AF:

0.398

Gnomad SAS

AF:

0.0939

Gnomad FIN

AF:

0.0953

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0839

Gnomad OTH

AF:

0.0727

GnomAD3 exomes

AF:

0.131

AC:

32835

AN:

250078

Hom.:

3734

AF XY:

0.123

AC XY:

16604

AN XY:

135088

show subpopulations

Gnomad AFR exome

AF:

0.0211

Gnomad AMR exome

AF:

0.284

Gnomad ASJ exome

AF:

0.0325

Gnomad EAS exome

AF:

0.402

Gnomad SAS exome

AF:

0.0848

Gnomad FIN exome

AF:

0.107

Gnomad NFE exome

AF:

0.0838

Gnomad OTH exome

AF:

0.101

GnomAD4 exome

AF:

0.0986

AC:

143670

AN:

1457076

Hom.:

10735

Cov.:

AF XY:

0.0971

AC XY:

70283

AN XY:

723896

show subpopulations

Gnomad4 AFR exome

AF:

0.0170

Gnomad4 AMR exome

AF:

0.274

Gnomad4 ASJ exome

AF:

0.0322

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.0846

Gnomad4 FIN exome

AF:

0.104

Gnomad4 NFE exome

AF:

0.0848

Gnomad4 OTH exome

AF:

0.0951

GnomAD4 genome

AF:

0.0900

AC:

13696

AN:

152094

Hom.:

1099

Cov.:

AF XY:

0.0936

AC XY:

6953

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.0255

Gnomad4 AMR

AF:

0.203

Gnomad4 ASJ

AF:

0.0288

Gnomad4 EAS

AF:

0.398

Gnomad4 SAS

AF:

0.0927

Gnomad4 FIN

AF:

0.0953

Gnomad4 NFE

AF:

0.0839

Gnomad4 OTH

AF:

0.0766

Alfa

AF:

0.0827

Hom.:

1127

Bravo

AF:

0.0966

Asia WGS

AF:

0.229

AC:

797

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

2.0

DANN

Benign

0.78

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