rs11544860
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002997.5(SDC1):c.-27C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 1,212,194 control chromosomes in the GnomAD database, including 2,595 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 0.044 ( 204 hom., cov: 33)
Exomes 𝑓: 0.065 ( 2391 hom. )
Consequence
SDC1
NM_002997.5 5_prime_UTR
NM_002997.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.648
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDC1 | NM_002997.5 | c.-27C>T | 5_prime_UTR_variant | 1/5 | ENST00000254351.9 | ||
SDC1 | NM_001006946.2 | c.-27C>T | 5_prime_UTR_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDC1 | ENST00000254351.9 | c.-27C>T | 5_prime_UTR_variant | 1/5 | 1 | NM_002997.5 | P1 | ||
SDC1 | ENST00000403076.5 | c.-27C>T | 5_prime_UTR_variant | 1/4 | 1 | ||||
SDC1 | ENST00000381150.5 | c.-27C>T | 5_prime_UTR_variant | 2/6 | 5 | P1 | |||
SDC1 | ENST00000447124.1 | c.-27C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0438 AC: 6655AN: 151878Hom.: 204 Cov.: 33
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GnomAD3 exomes AF: 0.0633 AC: 21AN: 332Hom.: 0 AF XY: 0.0798 AC XY: 15AN XY: 188
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GnomAD4 exome AF: 0.0652 AC: 69122AN: 1060208Hom.: 2391 Cov.: 31 AF XY: 0.0652 AC XY: 32722AN XY: 501660
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GnomAD4 genome ? AF: 0.0438 AC: 6656AN: 151986Hom.: 204 Cov.: 33 AF XY: 0.0421 AC XY: 3129AN XY: 74286
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ClinVar
Not reported inComputational scores
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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