chr11-4127054-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_001033.5(RRM1):c.1490G>A(p.Arg497His) variant causes a missense change. The variant allele was found at a frequency of 0.000366 in 1,610,124 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R497C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001033.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RRM1 | NM_001033.5 | c.1490G>A | p.Arg497His | missense_variant | 14/19 | ENST00000300738.10 | |
RRM1 | NM_001318064.1 | c.1199G>A | p.Arg400His | missense_variant | 13/18 | ||
RRM1 | NM_001330193.1 | c.824G>A | p.Arg275His | missense_variant | 8/13 | ||
RRM1 | NM_001318065.1 | c.476G>A | p.Arg159His | missense_variant | 8/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RRM1 | ENST00000300738.10 | c.1490G>A | p.Arg497His | missense_variant | 14/19 | 1 | NM_001033.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00204 AC: 310AN: 152094Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000545 AC: 135AN: 247628Hom.: 0 AF XY: 0.000374 AC XY: 50AN XY: 133820
GnomAD4 exome AF: 0.000192 AC: 280AN: 1457912Hom.: 1 Cov.: 31 AF XY: 0.000161 AC XY: 117AN XY: 725186
GnomAD4 genome ? AF: 0.00204 AC: 310AN: 152212Hom.: 1 Cov.: 32 AF XY: 0.00206 AC XY: 153AN XY: 74410
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at