chr2-203440174-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_213589.3(RAPH1):c.3016C>A(p.Pro1006Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_213589.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAPH1 | NM_213589.3 | c.3016C>A | p.Pro1006Thr | missense_variant | 14/14 | ENST00000319170.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAPH1 | ENST00000319170.10 | c.3016C>A | p.Pro1006Thr | missense_variant | 14/14 | 1 | NM_213589.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152142Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251030Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135748
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461558Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 727094
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152142Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.3016C>A (p.P1006T) alteration is located in exon 14 (coding exon 13) of the RAPH1 gene. This alteration results from a C to A substitution at nucleotide position 3016, causing the proline (P) at amino acid position 1006 to be replaced by a threonine (T). 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