rs10883465
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005063.5(SCD):c.*1497C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,018 control chromosomes in the GnomAD database, including 4,893 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 0.23 ( 4893 hom., cov: 32)
Exomes 𝑓: 0.14 ( 0 hom. )
Consequence
SCD
NM_005063.5 3_prime_UTR
NM_005063.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.727
Genes affected
SCD (HGNC:10571): (stearoyl-CoA desaturase) This gene encodes an enzyme involved in fatty acid biosynthesis, primarily the synthesis of oleic acid. The protein belongs to the fatty acid desaturase family and is an integral membrane protein located in the endoplasmic reticulum. Transcripts of approximately 3.9 and 5.2 kb, differing only by alternative polyadenlyation signals, have been detected. A gene encoding a similar enzyme is located on chromosome 4 and a pseudogene of this gene is located on chromosome 17. [provided by RefSeq, Sep 2015]
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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=-0.8).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCD | NM_005063.5 | c.*1497C>G | 3_prime_UTR_variant | 6/6 | ENST00000370355.3 | NP_005054.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCD | ENST00000370355.3 | c.*1497C>G | 3_prime_UTR_variant | 6/6 | 1 | NM_005063.5 | ENSP00000359380 | P1 |
Frequencies
GnomAD3 genomes AF: 0.234 AC: 35544AN: 151886Hom.: 4863 Cov.: 32
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GnomAD4 exome AF: 0.143 AC: 2AN: 14Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2AN XY: 10
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GnomAD4 genome AF: 0.234 AC: 35615AN: 152004Hom.: 4893 Cov.: 32 AF XY: 0.235 AC XY: 17475AN XY: 74288
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at