chr17-42990416-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173079.5(RUNDC1):c.956C>T(p.Thr319Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000582 in 1,613,848 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 (★). Synonymous variant affecting the same amino acid position (i.e. T319T) has been classified as Likely benign.
Frequency
Consequence
NM_173079.5 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 |
---|---|---|---|---|---|---|---|
RUNDC1 | NM_173079.5 | c.956C>T | p.Thr319Met | missense_variant | 4/5 | ENST00000361677.6 | |
RUNDC1 | NM_001321381.3 | c.962C>T | p.Thr321Met | missense_variant | 5/6 | ||
RUNDC1 | NM_001394222.1 | c.956C>T | p.Thr319Met | missense_variant | 4/5 | ||
RUNDC1 | XM_005257078.5 | c.962C>T | p.Thr321Met | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNDC1 | ENST00000361677.6 | c.956C>T | p.Thr319Met | missense_variant | 4/5 | 1 | NM_173079.5 | P1 | |
RUNDC1 | ENST00000589705.1 | c.754C>T | p.Arg252Cys | missense_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000957 AC: 24AN: 250654Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135670
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461610Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727088
GnomAD4 genome AF: 0.000131 AC: 20AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2023 | The c.956C>T (p.T319M) alteration is located in exon 4 (coding exon 4) of the RUNDC1 gene. This alteration results from a C to T substitution at nucleotide position 956, causing the threonine (T) at amino acid position 319 to be replaced by a methionine (M). 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