rs1539360
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_014654.4(SDC3):c.1188C>T(p.Gly396=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,612,534 control chromosomes in the GnomAD database, including 9,309 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.080 ( 653 hom., cov: 32)
Exomes 𝑓: 0.10 ( 8656 hom. )
Consequence
SDC3
NM_014654.4 synonymous
NM_014654.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.340
Genes affected
SDC3 (HGNC:10660): (syndecan 3) The protein encoded by this gene belongs to the syndecan proteoglycan family. It may play a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism. Allelic variants of this gene have been associated with obesity. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP7
Synonymous conserved (PhyloP=-0.34 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDC3 | NM_014654.4 | c.1188C>T | p.Gly396= | synonymous_variant | 5/5 | ENST00000339394.7 | NP_055469.3 | |
SDC3 | XM_011542463.1 | c.1155C>T | p.Gly385= | synonymous_variant | 5/5 | XP_011540765.1 | ||
SDC3 | XM_011542464.3 | c.1152C>T | p.Gly384= | synonymous_variant | 5/5 | XP_011540766.1 | ||
SDC3 | XM_011542466.2 | c.1062C>T | p.Gly354= | synonymous_variant | 5/5 | XP_011540768.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDC3 | ENST00000339394.7 | c.1188C>T | p.Gly396= | synonymous_variant | 5/5 | 1 | NM_014654.4 | ENSP00000344468 | P1 | |
SDC3 | ENST00000336798.11 | c.1014C>T | p.Gly338= | synonymous_variant | 3/3 | 1 | ENSP00000338346 |
Frequencies
GnomAD3 genomes AF: 0.0805 AC: 12232AN: 152010Hom.: 653 Cov.: 32
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GnomAD3 exomes AF: 0.0892 AC: 22399AN: 251216Hom.: 1166 AF XY: 0.0910 AC XY: 12350AN XY: 135778
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GnomAD4 exome AF: 0.105 AC: 153303AN: 1460406Hom.: 8656 Cov.: 31 AF XY: 0.104 AC XY: 75309AN XY: 726590
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GnomAD4 genome AF: 0.0804 AC: 12231AN: 152128Hom.: 653 Cov.: 32 AF XY: 0.0792 AC XY: 5891AN XY: 74358
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at