2-3696331-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018436.4(ALLC):c.724C>T(p.Arg242Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,612,698 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000059 ( 0 hom. )
Consequence
ALLC
NM_018436.4 missense
NM_018436.4 missense
Scores
4
8
5
Clinical Significance
Conservation
PhyloP100: 0.672
Genes affected
ALLC (HGNC:17377): (allantoicase) Allantoicase (EC 3.5.3.4) participates in the uric acid degradation pathway. Its enzymatic activity, like that of urate oxidase (MIM 191540), was lost during vertebrate evolution.[supplied by OMIM, Nov 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALLC | NM_018436.4 | c.724C>T | p.Arg242Trp | missense_variant | 9/12 | ENST00000252505.4 | NP_060906.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALLC | ENST00000252505.4 | c.724C>T | p.Arg242Trp | missense_variant | 9/12 | 1 | NM_018436.4 | ENSP00000252505.3 | ||
ALLC | ENST00000471711.1 | n.388C>T | non_coding_transcript_exon_variant | 3/6 | 3 | |||||
ALLC | ENST00000476389.5 | n.1309C>T | non_coding_transcript_exon_variant | 2/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152110Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000109 AC: 27AN: 248268Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134674
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GnomAD4 exome AF: 0.0000589 AC: 86AN: 1460470Hom.: 0 Cov.: 30 AF XY: 0.0000661 AC XY: 48AN XY: 726480
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GnomAD4 genome AF: 0.000112 AC: 17AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74436
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2024 | The c.724C>T (p.R242W) alteration is located in exon 9 (coding exon 8) of the ALLC gene. This alteration results from a C to T substitution at nucleotide position 724, causing the arginine (R) at amino acid position 242 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Uncertain
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at