rs3071
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005063.5(SCD):c.647+74A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 1,149,876 control chromosomes in the GnomAD database, including 50,783 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 0.24 ( 5535 hom., cov: 32)
Exomes 𝑓: 0.29 ( 45248 hom. )
Consequence
SCD
NM_005063.5 intron
NM_005063.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.365
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCD | NM_005063.5 | c.647+74A>C | intron_variant | ENST00000370355.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCD | ENST00000370355.3 | c.647+74A>C | intron_variant | 1 | NM_005063.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.240 AC: 36498AN: 151952Hom.: 5537 Cov.: 32
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GnomAD4 exome AF: 0.295 AC: 294261AN: 997804Hom.: 45248 AF XY: 0.296 AC XY: 150769AN XY: 509052
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GnomAD4 genome ? AF: 0.240 AC: 36496AN: 152072Hom.: 5535 Cov.: 32 AF XY: 0.247 AC XY: 18362AN XY: 74330
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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