16-72090670-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017853.3(TXNL4B):āc.80T>Cā(p.Val27Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00025 ( 0 hom., cov: 33)
Exomes š: 0.000029 ( 0 hom. )
Consequence
TXNL4B
NM_017853.3 missense
NM_017853.3 missense
Scores
7
10
2
Clinical Significance
Conservation
PhyloP100: 9.07
Genes affected
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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 | UniProt |
---|---|---|---|---|---|---|---|
TXNL4B | NM_017853.3 | c.80T>C | p.Val27Ala | missense_variant | 2/4 | ENST00000268483.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNL4B | ENST00000268483.8 | c.80T>C | p.Val27Ala | missense_variant | 2/4 | 1 | NM_017853.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152222Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251342Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135828
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GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727240
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GnomAD4 genome AF: 0.000250 AC: 38AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74372
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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 | May 01, 2024 | The c.80T>C (p.V27A) alteration is located in exon 2 (coding exon 1) of the TXNL4B gene. This alteration results from a T to C substitution at nucleotide position 80, causing the valine (V) at amino acid position 27 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
.;T;T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;D;.;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
.;M;M;M;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D;D;D
Sift4G
Uncertain
.;D;D;D;.
Polyphen
1.0
.;D;D;D;.
Vest4
0.88
MVP
MPC
0.017
ClinPred
D
GERP RS
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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