6-7891640-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030810.5(TXNDC5):c.713A>T(p.Glu238Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,613,910 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E238K) has been classified as Uncertain significance.
Frequency
Consequence
NM_030810.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNDC5 | NM_030810.5 | c.713A>T | p.Glu238Val | missense_variant | 5/10 | ENST00000379757.9 | |
BLOC1S5-TXNDC5 | NR_037616.1 | n.872A>T | non_coding_transcript_exon_variant | 8/13 | |||
TXNDC5 | NM_001145549.4 | c.389A>T | p.Glu130Val | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC5 | ENST00000379757.9 | c.713A>T | p.Glu238Val | missense_variant | 5/10 | 1 | NM_030810.5 | P1 | |
TXNDC5 | ENST00000473453.2 | c.389A>T | p.Glu130Val | missense_variant | 5/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000237 AC: 36AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251374Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135864
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461610Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727108
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 12, 2024 | The c.713A>T (p.E238V) alteration is located in exon 5 (coding exon 5) of the TXNDC5 gene. This alteration results from a A to T substitution at nucleotide position 713, causing the glutamic acid (E) at amino acid position 238 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at