rs11190480
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000370355.3(SCD):c.311-48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 1,590,678 control chromosomes in the GnomAD database, including 8,050 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 0.091 ( 682 hom., cov: 32)
Exomes 𝑓: 0.098 ( 7368 hom. )
Consequence
SCD
ENST00000370355.3 intron
ENST00000370355.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.559
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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCD | NM_005063.5 | c.311-48A>G | intron_variant | ENST00000370355.3 | NP_005054.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCD | ENST00000370355.3 | c.311-48A>G | intron_variant | 1 | NM_005063.5 | ENSP00000359380 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0912 AC: 13874AN: 152062Hom.: 685 Cov.: 32
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GnomAD3 exomes AF: 0.0934 AC: 22735AN: 243366Hom.: 1180 AF XY: 0.0966 AC XY: 12711AN XY: 131622
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GnomAD4 exome AF: 0.0983 AC: 141415AN: 1438498Hom.: 7368 Cov.: 28 AF XY: 0.0989 AC XY: 70562AN XY: 713690
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GnomAD4 genome AF: 0.0912 AC: 13877AN: 152180Hom.: 682 Cov.: 32 AF XY: 0.0906 AC XY: 6737AN XY: 74400
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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