8-23291518-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001136108.3(R3HCC1):c.1010C>T(p.Thr337Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000774 in 1,550,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T337A) has been classified as Likely benign.
Frequency
Consequence
NM_001136108.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
R3HCC1 | NM_001136108.3 | c.1010C>T | p.Thr337Met | missense_variant | Exon 5 of 8 | ENST00000265806.12 | NP_001129580.2 | |
R3HCC1 | NM_001301650.2 | c.884C>T | p.Thr295Met | missense_variant | Exon 6 of 9 | NP_001288579.1 | ||
R3HCC1 | NR_125897.1 | n.979C>T | non_coding_transcript_exon_variant | Exon 6 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
R3HCC1 | ENST00000265806.12 | c.1010C>T | p.Thr337Met | missense_variant | Exon 5 of 8 | 1 | NM_001136108.3 | ENSP00000265806.8 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156348Hom.: 0 AF XY: 0.0000241 AC XY: 2AN XY: 82866
GnomAD4 exome AF: 0.00000643 AC: 9AN: 1398658Hom.: 0 Cov.: 39 AF XY: 0.0000101 AC XY: 7AN XY: 689836
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.449C>T (p.T150M) alteration is located in exon 5 (coding exon 2) of the R3HCC1 gene. This alteration results from a C to T substitution at nucleotide position 449, causing the threonine (T) at amino acid position 150 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