chr1-109487042-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001350175.2(ATXN7L2):c.334C>T(p.Arg112Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000584 in 1,608,384 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000054 ( 0 hom. )
Consequence
ATXN7L2
NM_001350175.2 missense
NM_001350175.2 missense
Scores
9
10
Clinical Significance
Conservation
PhyloP100: 3.59
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.26844865).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATXN7L2 | NM_001350175.2 | c.334C>T | p.Arg112Trp | missense_variant | 4/11 | ENST00000683729.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATXN7L2 | ENST00000683729.1 | c.334C>T | p.Arg112Trp | missense_variant | 4/11 | NM_001350175.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152150Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000571 AC: 14AN: 245132Hom.: 0 AF XY: 0.0000677 AC XY: 9AN XY: 132870
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GnomAD4 exome AF: 0.0000536 AC: 78AN: 1456234Hom.: 0 Cov.: 31 AF XY: 0.0000594 AC XY: 43AN XY: 724224
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GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74326
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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 04, 2022 | The c.334C>T (p.R112W) alteration is located in exon 4 (coding exon 4) of the ATXN7L2 gene. This alteration results from a C to T substitution at nucleotide position 334, causing the arginine (R) at amino acid position 112 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
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Calibrated prediction
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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