rs13850
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001144757.3(SCG5):c.-32A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,322 control chromosomes in the GnomAD database, including 1,122 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.11 ( 1119 hom., cov: 32)
Exomes 𝑓: 0.21 ( 3 hom. )
Consequence
SCG5
NM_001144757.3 5_prime_UTR
NM_001144757.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.55
Genes affected
SCG5 (HGNC:10816): (secretogranin V) This gene encodes a secreted chaperone protein that prevents the aggregation of other secreted proteins, including proteins that are associated with neurodegenerative and metabolic disease. The encoded protein may be best known for its role in the trafficking and activation of prohormone convertase PC2 (encoded by Gene ID: 5126). Phosphorylation of the encoded protein has been shown to have an inhibitory effect on its chaperone function. This gene also produces a ARHGAP11A-SCG5 readthrough transcript and ARHGAP11A-SCG5 protein. [provided by RefSeq, Feb 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 15-32641754-A-T is Benign according to our data. Variant chr15-32641754-A-T is described in ClinVar as [Benign]. Clinvar id is 1287486.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCG5 | NM_001144757.3 | c.-32A>T | 5_prime_UTR_variant | 1/6 | ENST00000300175.9 | ||
ARHGAP11A-SCG5 | NM_001368319.1 | c.1236-1832A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCG5 | ENST00000300175.9 | c.-32A>T | 5_prime_UTR_variant | 1/6 | 1 | NM_001144757.3 | P1 | ||
SCG5 | ENST00000413748.6 | c.-32A>T | 5_prime_UTR_variant | 1/6 | 1 | ||||
SCG5 | ENST00000494364.5 | c.-32A>T | 5_prime_UTR_variant | 1/5 | 5 | ||||
SCG5 | ENST00000497208.5 | c.-32A>T | 5_prime_UTR_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.110 AC: 16674AN: 152086Hom.: 1119 Cov.: 32
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GnomAD4 exome AF: 0.207 AC: 24AN: 116Hom.: 3 Cov.: 0 AF XY: 0.207 AC XY: 17AN XY: 82
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GnomAD4 genome ? AF: 0.110 AC: 16671AN: 152206Hom.: 1119 Cov.: 32 AF XY: 0.107 AC XY: 7992AN XY: 74416
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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 | GeneDx | Jul 14, 2018 | - - |
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