5-134887855-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_024715.4(TXNDC15):c.264C>T(p.Gly88=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,008 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
TXNDC15
NM_024715.4 synonymous
NM_024715.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.05
Genes affected
TXNDC15 (HGNC:20652): (thioredoxin domain containing 15) This gene encodes a member of the thioredoxin superfamily. Members of this family are characterized by a conserved active motif called the thioredoxin fold that catalyzes disulfide bond formation and isomerization. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 5-134887855-C-T is Benign according to our data. Variant chr5-134887855-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1947875.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.05 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TXNDC15 | NM_024715.4 | c.264C>T | p.Gly88= | synonymous_variant | 2/5 | ENST00000358387.9 | NP_078991.3 | |
TXNDC15 | NM_001350735.2 | c.60C>T | p.Gly20= | synonymous_variant | 2/5 | NP_001337664.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TXNDC15 | ENST00000358387.9 | c.264C>T | p.Gly88= | synonymous_variant | 2/5 | 1 | NM_024715.4 | ENSP00000351157 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152122Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251418Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135898
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GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727248
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152122Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74294
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 13, 2022 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at