10-100360777-C-T
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_005063.5(SCD):c.924C>T(p.Tyr308=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0041 in 1,613,978 control chromosomes in the GnomAD database, including 206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.021 ( 108 hom., cov: 33)
Exomes 𝑓: 0.0024 ( 98 hom. )
Consequence
SCD
NM_005063.5 synonymous
NM_005063.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.418
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 -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
Variant 10-100360777-C-T is Benign according to our data. Variant chr10-100360777-C-T is described in ClinVar as [Benign]. Clinvar id is 773538.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.418 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0686 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCD | NM_005063.5 | c.924C>T | p.Tyr308= | synonymous_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.924C>T | p.Tyr308= | synonymous_variant | 6/6 | 1 | NM_005063.5 | ENSP00000359380 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0208 AC: 3169AN: 152204Hom.: 107 Cov.: 33
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GnomAD3 exomes AF: 0.00573 AC: 1439AN: 251130Hom.: 47 AF XY: 0.00429 AC XY: 582AN XY: 135740
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GnomAD4 exome AF: 0.00235 AC: 3438AN: 1461656Hom.: 98 Cov.: 31 AF XY: 0.00212 AC XY: 1539AN XY: 727142
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GnomAD4 genome AF: 0.0209 AC: 3178AN: 152322Hom.: 108 Cov.: 33 AF XY: 0.0201 AC XY: 1496AN XY: 74482
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
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CADD
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at