chr6-7884388-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030810.5(TXNDC5):āc.1147G>Cā(p.Ala383Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030810.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNDC5 | NM_030810.5 | c.1147G>C | p.Ala383Pro | missense_variant | 9/10 | ENST00000379757.9 | |
BLOC1S5-TXNDC5 | NR_037616.1 | n.1306G>C | non_coding_transcript_exon_variant | 12/13 | |||
TXNDC5 | NM_001145549.4 | c.823G>C | p.Ala275Pro | missense_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC5 | ENST00000379757.9 | c.1147G>C | p.Ala383Pro | missense_variant | 9/10 | 1 | NM_030810.5 | P1 | |
TXNDC5 | ENST00000473453.2 | c.823G>C | p.Ala275Pro | missense_variant | 9/10 | 1 | |||
TXNDC5 | ENST00000460138.5 | n.925G>C | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
TXNDC5 | ENST00000475802.1 | n.441G>C | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251484Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135914
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461858Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727228
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.1147G>C (p.A383P) alteration is located in exon 9 (coding exon 9) of the TXNDC5 gene. This alteration results from a G to C substitution at nucleotide position 1147, causing the alanine (A) at amino acid position 383 to be replaced by a proline (P). 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