4-78870926-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198892.2(BMP2K):c.1375C>G(p.His459Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,609,456 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H459L) has been classified as Uncertain significance.
Frequency
Consequence
NM_198892.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP2K | NM_198892.2 | c.1375C>G | p.His459Asp | missense_variant | 11/16 | ENST00000502613.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP2K | ENST00000502613.3 | c.1375C>G | p.His459Asp | missense_variant | 11/16 | 1 | NM_198892.2 | P1 | |
BMP2K | ENST00000502871.5 | c.1375C>G | p.His459Asp | missense_variant | 11/14 | 1 | |||
BMP2K | ENST00000389010.7 | c.*351C>G | 3_prime_UTR_variant, NMD_transcript_variant | 12/15 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000135 AC: 2AN: 147728Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461728Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727172
GnomAD4 genome ? AF: 0.0000135 AC: 2AN: 147728Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72194
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.1375C>G (p.H459D) alteration is located in exon 11 (coding exon 11) of the BMP2K gene. This alteration results from a C to G substitution at nucleotide position 1375, causing the histidine (H) at amino acid position 459 to be replaced by an aspartic acid (D). 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