chr11-85711173-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_206927.4(SYTL2):c.5685G>C(p.Lys1895Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00208 in 1,614,008 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 6 hom. )
Consequence
SYTL2
NM_206927.4 missense
NM_206927.4 missense
Scores
2
6
7
Clinical Significance
Conservation
PhyloP100: 2.85
Genes affected
SYTL2 (HGNC:15585): (synaptotagmin like 2) The protein encoded by this gene is a synaptotagmin-like protein (SLP) that belongs to a C2 domain-containing protein family. The SLP homology domain (SHD) of this protein has been shown to specifically bind the GTP-bound form of Ras-related protein Rab-27A (RAB27A). This protein plays a role in RAB27A-dependent vesicle trafficking and controls melanosome distribution in the cell periphery. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.008764625).
BP6
?
Variant 11-85711173-C-G is Benign according to our data. Variant chr11-85711173-C-G is described in ClinVar as [Benign]. Clinvar id is 714262.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYTL2 | NM_206927.4 | c.5685G>C | p.Lys1895Asn | missense_variant | 13/20 | ENST00000359152.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYTL2 | ENST00000359152.10 | c.5685G>C | p.Lys1895Asn | missense_variant | 13/20 | 1 | NM_206927.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00157 AC: 239AN: 152168Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00199 AC: 501AN: 251446Hom.: 3 AF XY: 0.00193 AC XY: 262AN XY: 135890
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GnomAD4 exome AF: 0.00213 AC: 3120AN: 1461722Hom.: 6 Cov.: 30 AF XY: 0.00211 AC XY: 1531AN XY: 727176
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GnomAD4 genome ? AF: 0.00157 AC: 239AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.00171 AC XY: 127AN XY: 74464
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;.;.;D;D;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
REVEL
Benign
Sift4G
Uncertain
D;D;D;T;T;T;D;D;D;.;.;.;.
Polyphen
D;.;D;.;.;P;D;D;.;.;.;.;.
Vest4
MutPred
0.25
.;.;.;.;.;.;Loss of ubiquitination at K590 (P = 0.0067);.;.;.;.;.;.;
MVP
MPC
0.094
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at