NM_030786.3:c.757T>C

Variant summary

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

The NM_030786.3(SYNC):ā€‹c.757T>Cā€‹(p.Cys253Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,551,336 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00011 ( 0 hom., cov: 28)
Exomes š‘“: 0.0000086 ( 0 hom. )

Consequence

SYNC
NM_030786.3 missense

Scores

4
7
8

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.73
Variant links:
Genes affected
SYNC (HGNC:28897): (syncoilin, intermediate filament protein) This gene encodes a member of the intermediate filament family which contains an N-terminal head domain, followed by a central coiled-coil region and a short C-terminal tail. The protein is highly expressed in skeletal and cardiac muscle. The protein links the dystrophin associated protein complex (DAPC) to desmin filaments in muscle and may have a structural role in striated muscle. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
SYNCNM_030786.3 linkc.757T>C p.Cys253Arg missense_variant Exon 2 of 5 ENST00000409190.8 NP_110413.3 Q9H7C4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SYNCENST00000409190.8 linkc.757T>C p.Cys253Arg missense_variant Exon 2 of 5 2 NM_030786.3 ENSP00000386439.3 Q9H7C4-1
SYNCENST00000373484.4 linkc.757T>C p.Cys253Arg missense_variant Exon 2 of 4 2 ENSP00000362583.3 Q9H7C4-2

Frequencies

GnomAD3 genomes
AF:
0.000106
AC:
16
AN:
151594
Hom.:
0
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.000364
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000209
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000381
AC:
6
AN:
157538
Hom.:
0
AF XY:
0.0000480
AC XY:
4
AN XY:
83258
show subpopulations
Gnomad AFR exome
AF:
0.000620
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000439
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000857
AC:
12
AN:
1399742
Hom.:
0
Cov.:
98
AF XY:
0.00000724
AC XY:
5
AN XY:
690380
show subpopulations
Gnomad4 AFR exome
AF:
0.000190
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000379
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000278
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.000106
AC:
16
AN:
151594
Hom.:
0
Cov.:
28
AF XY:
0.0000947
AC XY:
7
AN XY:
73954
show subpopulations
Gnomad4 AFR
AF:
0.000364
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000209
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000134
Hom.:
0
ExAC
AF:
0.0000523
AC:
2
Asia WGS
AF:
0.000866
AC:
3
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jan 18, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.757T>C (p.C253R) alteration is located in exon 2 (coding exon 2) of the SYNC gene. This alteration results from a T to C substitution at nucleotide position 757, causing the cysteine (C) at amino acid position 253 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.80
BayesDel_addAF
Uncertain
0.022
T
BayesDel_noAF
Pathogenic
0.16
CADD
Pathogenic
28
DANN
Benign
0.91
DEOGEN2
Benign
0.20
T;.
Eigen
Uncertain
0.29
Eigen_PC
Uncertain
0.33
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.81
T;T
M_CAP
Uncertain
0.18
D
MetaRNN
Uncertain
0.63
D;D
MetaSVM
Uncertain
-0.20
T
MutationAssessor
Benign
1.0
L;L
PrimateAI
Uncertain
0.70
T
PROVEAN
Benign
-2.0
N;N
REVEL
Pathogenic
0.75
Sift
Benign
1.0
T;T
Sift4G
Benign
0.42
T;T
Polyphen
1.0
D;D
Vest4
0.86
MVP
0.56
MPC
1.4
ClinPred
0.15
T
GERP RS
4.5
Varity_R
0.59
gMVP
0.65

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.

Other links and lift over

dbSNP: rs755842604; hg19: chr1-33160942; API