rs10165462
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000488524.1(REG1A):n.116T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 178,746 control chromosomes in the GnomAD database, including 11,335 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 0.31 ( 9428 hom., cov: 32)
Exomes 𝑓: 0.36 ( 1907 hom. )
Consequence
REG1A
ENST00000488524.1 non_coding_transcript_exon
ENST00000488524.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.541
Genes affected
REG1A (HGNC:9951): (regenerating family member 1 alpha) This gene is a type I subclass member of the Reg gene family. The Reg gene family is a multigene family grouped into four subclasses, types I, II, III and IV, based on the primary structures of the encoded proteins. This gene encodes a protein that is secreted by the exocrine pancreas. It is associated with islet cell regeneration and diabetogenesis and may be involved in pancreatic lithogenesis. Reg family members REG1B, REGL, PAP and this gene are tandemly clustered on chromosome 2p12 and may have arisen from the same ancestral gene by gene duplication. [provided by RefSeq, Jul 2008]
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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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
use as main transcript | n.79120477T>C | intergenic_region | ||||||
REG1A | NM_002909.5 | c.-84T>C | upstream_gene_variant | ENST00000233735.2 | NP_002900.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
REG1A | ENST00000488524.1 | n.116T>C | non_coding_transcript_exon_variant | 1/3 | 1 | |||||
REG1A | ENST00000233735.2 | c.-84T>C | upstream_gene_variant | 1 | NM_002909.5 | ENSP00000233735.1 | ||||
REG1A | ENST00000461579.1 | n.-13T>C | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.311 AC: 47227AN: 151930Hom.: 9432 Cov.: 32
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GnomAD4 exome AF: 0.358 AC: 9547AN: 26698Hom.: 1907 Cov.: 0 AF XY: 0.356 AC XY: 4818AN XY: 13532
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GnomAD4 genome AF: 0.311 AC: 47213AN: 152048Hom.: 9428 Cov.: 32 AF XY: 0.316 AC XY: 23499AN XY: 74294
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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