chr2-135641746-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001378107.1(R3HDM1):c.1430C>T(p.Ala477Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000192 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
R3HDM1 | NM_001378107.1 | c.1430C>T | p.Ala477Val | missense_variant | Exon 15 of 27 | ENST00000683871.1 | NP_001365036.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
R3HDM1 | ENST00000683871.1 | c.1430C>T | p.Ala477Val | missense_variant | Exon 15 of 27 | NM_001378107.1 | ENSP00000506980.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251336Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135842
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461804Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727208
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1430C>T (p.A477V) alteration is located in exon 15 (coding exon 13) of the R3HDM1 gene. This alteration results from a C to T substitution at nucleotide position 1430, causing the alanine (A) at amino acid position 477 to be replaced by a valine (V). 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