8-124486974-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_007218.4(RNF139):c.1325C>T(p.Thr442Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,970 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 (★).
Frequency
Consequence
NM_007218.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF139 | NM_007218.4 | c.1325C>T | p.Thr442Met | missense_variant | 2/2 | ENST00000303545.4 | |
RNF139 | XM_047421310.1 | c.944C>T | p.Thr315Met | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF139 | ENST00000303545.4 | c.1325C>T | p.Thr442Met | missense_variant | 2/2 | 1 | NM_007218.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250878Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135586
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461758Hom.: 0 Cov.: 34 AF XY: 0.0000193 AC XY: 14AN XY: 727192
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.1325C>T (p.T442M) alteration is located in exon 2 (coding exon 2) of the RNF139 gene. This alteration results from a C to T substitution at nucleotide position 1325, causing the threonine (T) at amino acid position 442 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