chr2-135651889-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001378107.1(R3HDM1):c.1885C>G(p.Pro629Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,486 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. P629S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378107.1 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
R3HDM1 | NM_001378107.1 | c.1885C>G | p.Pro629Ala | missense_variant | 18/27 | ENST00000683871.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
R3HDM1 | ENST00000683871.1 | c.1885C>G | p.Pro629Ala | missense_variant | 18/27 | NM_001378107.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248864Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134720
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461430Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727018
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.1780C>G (p.P594A) alteration is located in exon 17 (coding exon 15) of the R3HDM1 gene. This alteration results from a C to G substitution at nucleotide position 1780, causing the proline (P) at amino acid position 594 to be replaced by an alanine (A). 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