rs9502658
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BS1BS2
The NM_030810.5(TXNDC5):c.639C>T(p.Phe213=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00226 in 1,613,654 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.012 ( 36 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 35 hom. )
Consequence
TXNDC5
NM_030810.5 synonymous
NM_030810.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.73
Genes affected
TXNDC5 (HGNC:21073): (thioredoxin domain containing 5) This gene encodes a member of the disulfide isomerase (PDI) family of endoplasmic reticulum (ER) proteins that catalyze protein folding and thiol-disulfide interchange reactions. The encoded protein has an N-terminal endoplasmic reticulum (ER)-signal sequence, three catalytically active thioredoxin domains and a C-terminal ER-retention sequence. Its expression is induced by hypoxia and its role may be to protect hypoxic cells from apoptosis. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the neighboring upstream BLOC1S5 gene. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP7
?
Synonymous conserved (PhyloP=1.73 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0122 (1865/152306) while in subpopulation AFR AF= 0.0418 (1737/41542). AF 95% confidence interval is 0.0402. There are 36 homozygotes in gnomad4. There are 899 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 36 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNDC5 | NM_030810.5 | c.639C>T | p.Phe213= | synonymous_variant | 5/10 | ENST00000379757.9 | |
BLOC1S5-TXNDC5 | NR_037616.1 | n.798C>T | non_coding_transcript_exon_variant | 8/13 | |||
TXNDC5 | NM_001145549.4 | c.315C>T | p.Phe105= | synonymous_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC5 | ENST00000379757.9 | c.639C>T | p.Phe213= | synonymous_variant | 5/10 | 1 | NM_030810.5 | P1 | |
TXNDC5 | ENST00000473453.2 | c.315C>T | p.Phe105= | synonymous_variant | 5/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0123 AC: 1866AN: 152188Hom.: 36 Cov.: 33
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GnomAD3 exomes AF: 0.00287 AC: 722AN: 251152Hom.: 14 AF XY: 0.00200 AC XY: 271AN XY: 135772
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GnomAD4 exome AF: 0.00122 AC: 1789AN: 1461348Hom.: 35 Cov.: 30 AF XY: 0.000990 AC XY: 720AN XY: 726986
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GnomAD4 genome ? AF: 0.0122 AC: 1865AN: 152306Hom.: 36 Cov.: 33 AF XY: 0.0121 AC XY: 899AN XY: 74480
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at