2-20204196-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002997.5(SDC1):c.244G>A(p.Gly82Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00168 in 1,599,476 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 21 hom., cov: 30)
Exomes 𝑓: 0.00092 ( 13 hom. )
Consequence
SDC1
NM_002997.5 missense
NM_002997.5 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: -1.65
Genes affected
SDC1 (HGNC:10658): (syndecan 1) The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan and is a member of the syndecan proteoglycan family. The syndecans mediate cell binding, cell signaling, and cytoskeletal organization and syndecan receptors are required for internalization of the HIV-1 tat protein. The syndecan-1 protein functions as an integral membrane protein and participates in cell proliferation, cell migration and cell-matrix interactions via its receptor for extracellular matrix proteins. Altered syndecan-1 expression has been detected in several different tumor types. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode the same protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0022182167).
BP6
?
Variant 2-20204196-C-T is Benign according to our data. Variant chr2-20204196-C-T is described in ClinVar as [Benign]. Clinvar id is 716280.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00894 (1360/152106) while in subpopulation AFR AF= 0.03 (1243/41502). AF 95% confidence interval is 0.0286. There are 21 homozygotes in gnomad4. There are 630 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1360 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDC1 | NM_002997.5 | c.244G>A | p.Gly82Ser | missense_variant | 3/5 | ENST00000254351.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDC1 | ENST00000254351.9 | c.244G>A | p.Gly82Ser | missense_variant | 3/5 | 1 | NM_002997.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00895 AC: 1360AN: 151988Hom.: 21 Cov.: 30
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GnomAD3 exomes AF: 0.00244 AC: 584AN: 239790Hom.: 5 AF XY: 0.00162 AC XY: 211AN XY: 130486
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GnomAD4 exome AF: 0.000917 AC: 1327AN: 1447370Hom.: 13 Cov.: 38 AF XY: 0.000772 AC XY: 556AN XY: 720456
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GnomAD4 genome ? AF: 0.00894 AC: 1360AN: 152106Hom.: 21 Cov.: 30 AF XY: 0.00847 AC XY: 630AN XY: 74342
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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 | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;.
Polyphen
B;B;B;.
Vest4
MVP
MPC
0.24
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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