22-39377595-C-T

Variant names:

• chr22-39377595-C-T
• rs193920982
• NM_004711.5:c.483+1398C>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_145738.3(SYNGR1):​c.487-3C>T variant causes a splice region, intron change. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: SYNGR1 NM_145738.3 splice_region, intron
• Scores: Splicing: ADA: 0.9083
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 5.05

Genes affected

SYNGR1 (HGNC:11498): (synaptogyrin 1) This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced variants encoding three different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SYNGR1	NM_004711.5	c.483+1398C>T		intron_variant	Intron 3 of 3	ENST00000328933.10	NP_004702.2
SYNGR1	NM_145738.3	c.487-3C>T		splice_region_variant, intron_variant	Intron 3 of 3		NP_663791.1
SYNGR1	NM_145731.4	c.484-3C>T		splice_region_variant, intron_variant	Intron 3 of 3		NP_663783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SYNGR1	ENST00000328933.10	c.483+1398C>T		intron_variant	Intron 3 of 3	1	NM_004711.5	ENSP00000332287.5
SYNGR1	ENST00000381535.4	c.487-3C>T		splice_region_variant, intron_variant	Intron 3 of 3	1		ENSP00000370946.4
SYNGR1	ENST00000318801.8	c.484-3C>T		splice_region_variant, intron_variant	Intron 3 of 3	1		ENSP00000318845.4
SYNGR1	ENST00000415332.1	n.*156-3C>T		splice_region_variant, intron_variant	Intron 3 of 3	3		ENSP00000412442.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Malignant tumor of prostate Uncertain:1

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Science for Life laboratory, Karolinska Institutet

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.060
CADD	Pathogenic	26
DANN	Benign	0.97

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.91
dbscSNV1_RF	Benign	0.68
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

Other links and lift over

dbSNP: rs193920982; hg19: chr22-39773600;