chr14-52455433-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020784.3(TXNDC16):c.1733C>T(p.Ala578Val) variant causes a missense change. The variant allele was found at a frequency of 0.000549 in 1,613,880 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00040 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00056 ( 0 hom. )
Consequence
TXNDC16
NM_020784.3 missense
NM_020784.3 missense
Scores
3
7
9
Clinical Significance
Conservation
PhyloP100: 4.86
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 |
---|---|---|---|---|---|---|---|
TXNDC16 | NM_020784.3 | c.1733C>T | p.Ala578Val | missense_variant | 18/21 | ENST00000281741.9 | |
TXNDC16 | NM_001160047.2 | c.1718C>T | p.Ala573Val | missense_variant | 18/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC16 | ENST00000281741.9 | c.1733C>T | p.Ala578Val | missense_variant | 18/21 | 1 | NM_020784.3 | P1 | |
TXNDC16 | ENST00000554399.1 | n.208-14709C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
TXNDC16 | ENST00000555312.1 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 61AN: 152154Hom.: 1 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.000406 AC: 102AN: 251264Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135790
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GnomAD4 exome AF: 0.000564 AC: 825AN: 1461726Hom.: 0 Cov.: 30 AF XY: 0.000535 AC XY: 389AN XY: 727162
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GnomAD4 genome ? AF: 0.000401 AC: 61AN: 152154Hom.: 1 Cov.: 32 AF XY: 0.000323 AC XY: 24AN XY: 74344
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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 | Nov 01, 2022 | The c.1733C>T (p.A578V) alteration is located in exon 18 (coding exon 16) of the TXNDC16 gene. This alteration results from a C to T substitution at nucleotide position 1733, causing the alanine (A) at amino acid position 578 to be replaced by a valine (V). 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
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Pathogenic
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at