rs202159001
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001202.6(BMP4):c.304A>G(p.Thr102Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000187 in 1,604,382 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 (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T102I) has been classified as Likely benign.
Frequency
Consequence
NM_001202.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP4 | NM_001202.6 | c.304A>G | p.Thr102Ala | missense_variant | 3/4 | ENST00000245451.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP4 | ENST00000245451.9 | c.304A>G | p.Thr102Ala | missense_variant | 3/4 | 1 | NM_001202.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000824 AC: 2AN: 242804Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131934
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1452128Hom.: 0 Cov.: 32 AF XY: 0.0000180 AC XY: 13AN XY: 722852
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74438
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 21, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at