rs34183594
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001200.4(BMP2):āc.482T>Cā(p.Leu161Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000452 in 1,614,178 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001200.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP2 | NM_001200.4 | c.482T>C | p.Leu161Ser | missense_variant | 3/3 | ENST00000378827.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP2 | ENST00000378827.5 | c.482T>C | p.Leu161Ser | missense_variant | 3/3 | 1 | NM_001200.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152192Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251320Hom.: 1 AF XY: 0.0000809 AC XY: 11AN XY: 135896
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461868Hom.: 0 Cov.: 30 AF XY: 0.0000481 AC XY: 35AN XY: 727236
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152310Hom.: 1 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74484
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | This sequence change replaces leucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 161 of the BMP2 protein (p.Leu161Ser). This variant is present in population databases (rs34183594, gnomAD 0.05%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with BMP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1038630). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at