rs5754216

Variant names:

• chr22-32692207-C-A
• rs5754216
• NM_003490.4:c.712-95471G>T

Your query was ambiguous. Multiple possible variants found:

• chr22-32692207-C-A
• chr22-32692207-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_003490.4(SYN3):​c.712-95471G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 1.0 (68562 hom., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: SYN3 NM_003490.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 1 publications found

Genes affected

SYN3 (HGNC:11496): (synapsin III) This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. The protein encoded by this gene shares the synapsin family domain model, with domains A, C, and E exhibiting the highest degree of conservation. The protein contains a unique domain J, located between domains C and E. Based on this gene's localization to 22q12.3, a possible schizophrenia susceptibility locus, and the established neurobiological roles of the synapsins, this family member may represent a candidate gene for schizophrenia. The TIMP3 gene is located within an intron of this gene and is transcribed in the opposite direction. Alternative splicing of this gene results in multiple splice variants that encode different isoforms. [provided by RefSeq, Oct 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003490.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYN3	NM_003490.4	MANE Select	c.712-95471G>T		intron	N/A	NP_003481.3
	SYN3	NM_001369907.1		c.712-95471G>T		intron	N/A	NP_001356836.1	O14994
	SYN3	NM_001369908.1		c.712-95471G>T		intron	N/A	NP_001356837.1	O14994

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SYN3	ENST00000358763.7	TSL:5 MANE Select	c.712-95471G>T		intron	N/A	ENSP00000351614.2	O14994
	SYN3	ENST00000462268.1	TSL:3	n.226-62339G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 1.00 AC: 137100 AN: 137102 Hom.: 68549 Cov.: 17

Gnomad AFR AF: 1.00

Gnomad AMI AF: 1.00

Gnomad AMR AF: 1.00

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 1.00

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 1.00 AC: 137126 AN: 137128 Hom.: 68562 Cov.: 17 AF XY: 1.00 AC XY: 65659 AN XY: 65660

African (AFR) AF: 1.00 AC: 36136 AN: 36136

American (AMR) AF: 1.00 AC: 13508 AN: 13508

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3380 AN: 3380

East Asian (EAS) AF: 1.00 AC: 4574 AN: 4574

South Asian (SAS) AF: 1.00 AC: 4140 AN: 4140

European-Finnish (FIN) AF: 1.00 AC: 7675 AN: 7676

Middle Eastern (MID) AF: 1.00 AC: 260 AN: 260

European-Non Finnish (NFE) AF: 1.00 AC: 64707 AN: 64708

Other (OTH) AF: 1.00 AC: 1854 AN: 1854

Alfa AF: 1.00 Hom.: 5931

Bravo AF: 1.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.31
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5754216; hg19: chr22-33088193;