chr2-219539613-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_024536.6(CHPF):c.2098G>A(p.Glu700Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000425 in 1,613,760 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E700V) has been classified as Uncertain significance.
Frequency
Consequence
NM_024536.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHPF | NM_024536.6 | c.2098G>A | p.Glu700Lys | missense_variant | Exon 4 of 4 | ENST00000243776.11 | NP_078812.3 | |
CHPF | NM_001195731.2 | c.1612G>A | p.Glu538Lys | missense_variant | Exon 4 of 4 | NP_001182660.2 | ||
CHPF | XM_011511838.4 | c.1225G>A | p.Glu409Lys | missense_variant | Exon 3 of 3 | XP_011510140.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000374 AC: 57AN: 152240Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000244 AC: 61AN: 250000Hom.: 0 AF XY: 0.000251 AC XY: 34AN XY: 135384
GnomAD4 exome AF: 0.000430 AC: 629AN: 1461520Hom.: 0 Cov.: 30 AF XY: 0.000397 AC XY: 289AN XY: 727086
GnomAD4 genome AF: 0.000374 AC: 57AN: 152240Hom.: 0 Cov.: 34 AF XY: 0.000282 AC XY: 21AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2098G>A (p.E700K) 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 2098, causing the glutamic acid (E) at amino acid position 700 to be replaced by a lysine (K). 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