1-32695311-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_030786.3(SYNC):​c.787C>T​(p.Arg263Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00468 in 1,551,630 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0027 ( 2 hom., cov: 28)
Exomes 𝑓: 0.0049 ( 40 hom. )

Consequence

SYNC
NM_030786.3 missense

Scores

1
12
6

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.61
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 Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0066640675).
BP6
Variant 1-32695311-G-A is Benign according to our data. Variant chr1-32695311-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3770462.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SYNCNM_030786.3 linkc.787C>T p.Arg263Cys 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.787C>T p.Arg263Cys missense_variant Exon 2 of 5 2 NM_030786.3 ENSP00000386439.3 Q9H7C4-1
SYNCENST00000373484.4 linkc.787C>T p.Arg263Cys missense_variant Exon 2 of 4 2 ENSP00000362583.3 Q9H7C4-2

Frequencies

GnomAD3 genomes
AF:
0.00265
AC:
403
AN:
151840
Hom.:
2
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.000774
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00158
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00561
Gnomad FIN
AF:
0.00161
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00426
Gnomad OTH
AF:
0.00480
GnomAD3 exomes
AF:
0.00362
AC:
571
AN:
157578
Hom.:
3
AF XY:
0.00402
AC XY:
335
AN XY:
83308
show subpopulations
Gnomad AFR exome
AF:
0.000748
Gnomad AMR exome
AF:
0.00174
Gnomad ASJ exome
AF:
0.000589
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00711
Gnomad FIN exome
AF:
0.00112
Gnomad NFE exome
AF:
0.00531
Gnomad OTH exome
AF:
0.00247
GnomAD4 exome
AF:
0.00490
AC:
6859
AN:
1399672
Hom.:
40
Cov.:
98
AF XY:
0.00509
AC XY:
3516
AN XY:
690346
show subpopulations
Gnomad4 AFR exome
AF:
0.000728
Gnomad4 AMR exome
AF:
0.00162
Gnomad4 ASJ exome
AF:
0.000953
Gnomad4 EAS exome
AF:
0.0000280
Gnomad4 SAS exome
AF:
0.00762
Gnomad4 FIN exome
AF:
0.00120
Gnomad4 NFE exome
AF:
0.00539
Gnomad4 OTH exome
AF:
0.00442
GnomAD4 genome
AF:
0.00265
AC:
403
AN:
151958
Hom.:
2
Cov.:
28
AF XY:
0.00271
AC XY:
201
AN XY:
74248
show subpopulations
Gnomad4 AFR
AF:
0.000772
Gnomad4 AMR
AF:
0.00158
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00561
Gnomad4 FIN
AF:
0.00161
Gnomad4 NFE
AF:
0.00426
Gnomad4 OTH
AF:
0.00475
Alfa
AF:
0.00406
Hom.:
5
Bravo
AF:
0.00262
TwinsUK
AF:
0.00647
AC:
24
ALSPAC
AF:
0.00389
AC:
15
ESP6500AA
AF:
0.000723
AC:
1
ESP6500EA
AF:
0.00283
AC:
9
ExAC
AF:
0.00269
AC:
131
Asia WGS
AF:
0.00318
AC:
11
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

SYNC: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Uncertain
-0.050
CADD
Pathogenic
29
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.45
T;.
Eigen
Uncertain
0.38
Eigen_PC
Uncertain
0.40
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.89
D;D
M_CAP
Uncertain
0.088
D
MetaRNN
Benign
0.0067
T;T
MetaSVM
Uncertain
0.26
D
MutationAssessor
Benign
0.55
N;N
PrimateAI
Benign
0.33
T
PROVEAN
Uncertain
-3.4
D;D
REVEL
Uncertain
0.60
Sift
Uncertain
0.013
D;D
Sift4G
Uncertain
0.0080
D;D
Polyphen
1.0
D;D
Vest4
0.54
MVP
0.57
MPC
1.2
ClinPred
0.022
T
GERP RS
4.5
Varity_R
0.27
gMVP
0.37

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: rs41265855; hg19: chr1-33160912; API