2-232456931-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001631.5(ALPI):c.333C>T(p.Ser111=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 1,613,426 control chromosomes in the GnomAD database, including 6,464 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.094 ( 717 hom., cov: 32)
Exomes 𝑓: 0.087 ( 5747 hom. )
Consequence
ALPI
NM_001631.5 synonymous
NM_001631.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.02
Genes affected
ALPI (HGNC:437): (alkaline phosphatase, intestinal) There are at least four distinct but related alkaline phosphatases: intestinal, placental, placental-like, and liver/bone/kidney (tissue non-specific). The intestinal alkaline phosphatase gene encodes a digestive brush-border enzyme. This enzyme is a component of the gut mucosal defense system and is thought to function in the detoxification of lipopolysaccharide, and in the prevention of bacterial translocation in the gut. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BP6
Variant 2-232456931-C-T is Benign according to our data. Variant chr2-232456931-C-T is described in ClinVar as [Benign]. Clinvar id is 3055586.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.02 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALPI | NM_001631.5 | c.333C>T | p.Ser111= | synonymous_variant | 4/11 | ENST00000295463.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALPI | ENST00000295463.4 | c.333C>T | p.Ser111= | synonymous_variant | 4/11 | 1 | NM_001631.5 | P1 | |
ALPI | ENST00000457560.1 | c.*262C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0942 AC: 14320AN: 152094Hom.: 719 Cov.: 32
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GnomAD3 exomes AF: 0.0892 AC: 22348AN: 250516Hom.: 1114 AF XY: 0.0897 AC XY: 12155AN XY: 135576
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GnomAD4 exome AF: 0.0867 AC: 126664AN: 1461214Hom.: 5747 Cov.: 34 AF XY: 0.0870 AC XY: 63256AN XY: 726920
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GnomAD4 genome AF: 0.0941 AC: 14318AN: 152212Hom.: 717 Cov.: 32 AF XY: 0.0942 AC XY: 7008AN XY: 74402
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
ALPI-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 20, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Benign
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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