6-7888722-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000379757.9(TXNDC5):c.946G>A(p.Glu316Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,612,572 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000379757.9 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TXNDC5 | NM_030810.5 | c.946G>A | p.Glu316Lys | missense_variant | 7/10 | ENST00000379757.9 | NP_110437.2 | |
BLOC1S5-TXNDC5 | NR_037616.1 | n.1105G>A | non_coding_transcript_exon_variant | 10/13 | ||||
TXNDC5 | NM_001145549.4 | c.622G>A | p.Glu208Lys | missense_variant | 7/10 | NP_001139021.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TXNDC5 | ENST00000379757.9 | c.946G>A | p.Glu316Lys | missense_variant | 7/10 | 1 | NM_030810.5 | ENSP00000369081 | P1 | |
TXNDC5 | ENST00000473453.2 | c.622G>A | p.Glu208Lys | missense_variant | 7/10 | 1 | ENSP00000420784 | |||
TXNDC5 | ENST00000460138.5 | n.724G>A | non_coding_transcript_exon_variant | 1/4 | 2 | |||||
TXNDC5 | ENST00000475802.1 | n.240G>A | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249326Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134878
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460242Hom.: 0 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726406
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2024 | The c.946G>A (p.E316K) alteration is located in exon 7 (coding exon 7) of the TXNDC5 gene. This alteration results from a G to A substitution at nucleotide position 946, causing the glutamic acid (E) at amino acid position 316 to be replaced by a lysine (K). 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