chr1-39522438-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_181809.4(BMP8A):c.904C>T(p.Arg302Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,126 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R302H) has been classified as Uncertain significance.
Frequency
Consequence
NM_181809.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP8A | NM_181809.4 | c.904C>T | p.Arg302Cys | missense_variant | 5/7 | ENST00000331593.6 | |
PPIEL | NR_003929.2 | n.2479G>A | non_coding_transcript_exon_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP8A | ENST00000331593.6 | c.904C>T | p.Arg302Cys | missense_variant | 5/7 | 1 | NM_181809.4 | P1 | |
PPIEL | ENST00000692918.1 | n.1125G>A | non_coding_transcript_exon_variant | 9/9 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151860Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461266Hom.: 0 Cov.: 36 AF XY: 0.00000963 AC XY: 7AN XY: 726894
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151860Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74148
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.904C>T (p.R302C) alteration is located in exon 5 (coding exon 5) of the BMP8A gene. This alteration results from a C to T substitution at nucleotide position 904, causing the arginine (R) at amino acid position 302 to be replaced by a cysteine (C). 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