2-219539522-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024536.6(CHPF):c.2189G>A(p.Arg730His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000273 in 1,613,764 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★).
Frequency
Consequence
NM_024536.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHPF | NM_024536.6 | c.2189G>A | p.Arg730His | missense_variant | Exon 4 of 4 | ENST00000243776.11 | NP_078812.3 | |
CHPF | NM_001195731.2 | c.1703G>A | p.Arg568His | missense_variant | Exon 4 of 4 | NP_001182660.2 | ||
CHPF | XM_011511838.4 | c.1316G>A | p.Arg439His | missense_variant | Exon 3 of 3 | XP_011510140.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000539 AC: 82AN: 152250Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000363 AC: 91AN: 250428Hom.: 0 AF XY: 0.000295 AC XY: 40AN XY: 135618
GnomAD4 exome AF: 0.000246 AC: 360AN: 1461396Hom.: 2 Cov.: 30 AF XY: 0.000241 AC XY: 175AN XY: 727032
GnomAD4 genome AF: 0.000532 AC: 81AN: 152368Hom.: 0 Cov.: 34 AF XY: 0.000510 AC XY: 38AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2189G>A (p.R730H) alteration is located in exon 4 (coding exon 4) of the CHPF gene. This alteration results from a G to A substitution at nucleotide position 2189, causing the arginine (R) at amino acid position 730 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