chr6-7889564-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_030810.5(TXNDC5):āc.750C>Gā(p.His250Gln) 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 1,613,192 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
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TXNDC5 | NM_030810.5 | c.750C>G | p.His250Gln | missense_variant | 6/10 | ENST00000379757.9 | NP_110437.2 | |
BLOC1S5-TXNDC5 | NR_037616.1 | n.909C>G | non_coding_transcript_exon_variant | 9/13 | ||||
TXNDC5 | NM_001145549.4 | c.426C>G | p.His142Gln | missense_variant | 6/10 | NP_001139021.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TXNDC5 | ENST00000379757.9 | c.750C>G | p.His250Gln | missense_variant | 6/10 | 1 | NM_030810.5 | ENSP00000369081 | P1 | |
TXNDC5 | ENST00000473453.2 | c.426C>G | p.His142Gln | missense_variant | 6/10 | 1 | ENSP00000420784 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251342Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135872
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460964Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 726560
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2022 | The c.750C>G (p.H250Q) alteration is located in exon 6 (coding exon 6) of the TXNDC5 gene. This alteration results from a C to G substitution at nucleotide position 750, causing the histidine (H) at amino acid position 250 to be replaced by a glutamine (Q). 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