chr15-74850420-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005697.5(SCAMP2):c.632+94A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,117,448 control chromosomes in the GnomAD database, including 10,129 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 0.12 ( 1271 hom., cov: 32)
Exomes 𝑓: 0.13 ( 8858 hom. )
Consequence
SCAMP2
NM_005697.5 intron
NM_005697.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.345
Genes affected
SCAMP2 (HGNC:10564): (secretory carrier membrane protein 2) This gene product belongs to the SCAMP family of proteins which are secretory carrier membrane proteins. They function as carriers to the cell surface in post-golgi recycling pathways. Different family members are highly related products of distinct genes, and are usually expressed together. These findings suggest that the SCAMPs may function at the same site during vesicular transport rather than in separate pathways. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAMP2 | NM_005697.5 | c.632+94A>C | intron_variant | ENST00000268099.13 | |||
SCAMP2 | NM_001320778.2 | c.761+94A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAMP2 | ENST00000268099.13 | c.632+94A>C | intron_variant | 1 | NM_005697.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.119 AC: 18110AN: 151752Hom.: 1272 Cov.: 32
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GnomAD4 exome AF: 0.128 AC: 123904AN: 965572Hom.: 8858 AF XY: 0.129 AC XY: 63693AN XY: 494986
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GnomAD4 genome AF: 0.119 AC: 18103AN: 151876Hom.: 1271 Cov.: 32 AF XY: 0.124 AC XY: 9191AN XY: 74210
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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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at