chr6-7888793-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_030810.5(TXNDC5):c.875C>T(p.Ser292Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_030810.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNDC5 | NM_030810.5 | c.875C>T | p.Ser292Leu | missense_variant | 7/10 | ENST00000379757.9 | |
BLOC1S5-TXNDC5 | NR_037616.1 | n.1034C>T | non_coding_transcript_exon_variant | 10/13 | |||
TXNDC5 | NM_001145549.4 | c.551C>T | p.Ser184Leu | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC5 | ENST00000379757.9 | c.875C>T | p.Ser292Leu | missense_variant | 7/10 | 1 | NM_030810.5 | P1 | |
TXNDC5 | ENST00000473453.2 | c.551C>T | p.Ser184Leu | missense_variant | 7/10 | 1 | |||
TXNDC5 | ENST00000460138.5 | n.653C>T | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
TXNDC5 | ENST00000475802.1 | n.169C>T | non_coding_transcript_exon_variant | 1/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251160Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135728
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461784Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727184
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74370
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at