NM_005014.3:c.1007G>A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005014.3(OMD):c.1007G>A(p.Arg336His) variant causes a missense change. The variant allele was found at a frequency of 0.0000886 in 1,613,396 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005014.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OMD | ENST00000375550.5 | c.1007G>A | p.Arg336His | missense_variant | Exon 3 of 3 | 1 | NM_005014.3 | ENSP00000364700.4 | ||
CENPP | ENST00000375587.8 | c.564+35552C>T | intron_variant | Intron 5 of 7 | 1 | NM_001012267.3 | ENSP00000364737.3 |
Frequencies
GnomAD3 genomes AF: 0.0000790 AC: 12AN: 151982Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250520Hom.: 1 AF XY: 0.000199 AC XY: 27AN XY: 135392
GnomAD4 exome AF: 0.0000903 AC: 132AN: 1461296Hom.: 3 Cov.: 31 AF XY: 0.000121 AC XY: 88AN XY: 726968
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1007G>A (p.R336H) alteration is located in exon 3 (coding exon 2) of the OMD gene. This alteration results from a G to A substitution at nucleotide position 1007, causing the arginine (R) at amino acid position 336 to be replaced by a histidine (H). 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