NM_144979.5:c.29A>T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144979.5(RBM46):c.29A>T(p.Asn10Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_144979.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBM46 | ENST00000281722.8 | c.29A>T | p.Asn10Ile | missense_variant | Exon 2 of 5 | 1 | NM_144979.5 | ENSP00000281722.3 | ||
RBM46 | ENST00000514866.5 | c.29A>T | p.Asn10Ile | missense_variant | Exon 2 of 6 | 2 | ENSP00000424500.1 | |||
RBM46 | ENST00000510397.5 | c.29A>T | p.Asn10Ile | missense_variant | Exon 2 of 5 | 2 | ENSP00000422813.1 | |||
RBM46 | ENST00000512640.1 | c.29A>T | p.Asn10Ile | missense_variant | Exon 2 of 3 | 4 | ENSP00000426672.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248794Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134404
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459666Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 726068
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.29A>T (p.N10I) alteration is located in exon 2 (coding exon 1) of the RBM46 gene. This alteration results from a A to T substitution at nucleotide position 29, causing the asparagine (N) at amino acid position 10 to be replaced by an isoleucine (I). 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