chr16-1992038-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_004209.6(SYNGR3):​c.164C>T​(p.Pro55Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,428,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P55R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

SYNGR3
NM_004209.6 missense

Scores

1
5
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.51
Variant links:
Genes affected
SYNGR3 (HGNC:11501): (synaptogyrin 3) This gene encodes an integral membrane protein. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it is a synaptic vesicle protein that also interacts with the dopamine transporter. The gene product belongs to the synaptogyrin gene family. [provided by RefSeq, Dec 2010]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.34529597).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SYNGR3NM_004209.6 linkc.164C>T p.Pro55Leu missense_variant Exon 2 of 4 ENST00000248121.7 NP_004200.2 O43761

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SYNGR3ENST00000248121.7 linkc.164C>T p.Pro55Leu missense_variant Exon 2 of 4 1 NM_004209.6 ENSP00000248121.2 O43761
SYNGR3ENST00000568896.1 linkc.284C>T p.Pro95Leu missense_variant Exon 3 of 4 5 ENSP00000454756.1 H3BNA6
SYNGR3ENST00000563869.1 linkc.96C>T p.Pro32Pro synonymous_variant Exon 2 of 4 2 ENSP00000455344.1 H3BPJ5
SYNGR3ENST00000562045 linkc.-102C>T 5_prime_UTR_variant Exon 1 of 3 2 ENSP00000455577.1 H3BQ28

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000140
AC:
2
AN:
1428584
Hom.:
0
Cov.:
31
AF XY:
0.00000282
AC XY:
2
AN XY:
708010
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000121
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.11e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Uncertain
0.071
D
BayesDel_noAF
Benign
-0.14
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.091
T;.;T
Eigen
Benign
0.18
Eigen_PC
Benign
0.084
FATHMM_MKL
Benign
0.76
D
LIST_S2
Benign
0.72
T;T;T
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.35
T;T;T
MetaSVM
Benign
-0.56
T
MutationAssessor
Uncertain
2.2
M;.;.
PrimateAI
Pathogenic
0.81
D
PROVEAN
Uncertain
-3.9
D;.;D
REVEL
Benign
0.20
Sift
Benign
0.19
T;.;D
Sift4G
Benign
0.17
T;D;T
Polyphen
1.0
D;.;.
Vest4
0.45
MutPred
0.27
Loss of disorder (P = 0.0588);Loss of disorder (P = 0.0588);.;
MVP
0.71
MPC
0.94
ClinPred
0.96
D
GERP RS
4.3
Varity_R
0.23
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-2042039; API