chr3-47414034-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_012235.4(SCAP):c.3660C>G(p.Gly1220=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000342 in 1,613,300 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 1 hom. )
Consequence
SCAP
NM_012235.4 synonymous
NM_012235.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.97
Genes affected
SCAP (HGNC:30634): (SREBF chaperone) This gene encodes a protein with a sterol sensing domain (SSD) and seven WD domains. In the presence of cholesterol, this protein binds to sterol regulatory element binding proteins (SREBPs) and mediates their transport from the ER to the Golgi. The SREBPs are then proteolytically cleaved and regulate sterol biosynthesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 3-47414034-G-C is Benign according to our data. Variant chr3-47414034-G-C is described in ClinVar as [Benign]. Clinvar id is 724329.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.97 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAP | NM_012235.4 | c.3660C>G | p.Gly1220= | synonymous_variant | 23/23 | ENST00000265565.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAP | ENST00000265565.10 | c.3660C>G | p.Gly1220= | synonymous_variant | 23/23 | 1 | NM_012235.4 | P1 | |
SCAP | ENST00000648151.1 | c.3660C>G | p.Gly1220= | synonymous_variant | 24/24 | P1 | |||
SCAP | ENST00000320017.10 | c.*2374C>G | 3_prime_UTR_variant, NMD_transcript_variant | 18/18 | 2 | ||||
SCAP | ENST00000441517.6 | c.*2806C>G | 3_prime_UTR_variant, NMD_transcript_variant | 20/20 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00185 AC: 281AN: 152220Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000459 AC: 115AN: 250452Hom.: 1 AF XY: 0.000280 AC XY: 38AN XY: 135660
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GnomAD4 exome AF: 0.000185 AC: 271AN: 1460962Hom.: 1 Cov.: 32 AF XY: 0.000160 AC XY: 116AN XY: 726758
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at