8-22165483-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4BP6_ModerateBP7
The NM_006129.5(BMP1):c.78C>T(p.Ala26=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000629 in 1,590,424 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A26A) has been classified as Likely benign.
Frequency
Consequence
NM_006129.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP1 | NM_006129.5 | c.78C>T | p.Ala26= | synonymous_variant | 1/20 | ENST00000306385.10 | |
BMP1 | NM_001199.4 | c.78C>T | p.Ala26= | synonymous_variant | 1/16 | ENST00000306349.13 | |
BMP1 | NR_033403.2 | n.112C>T | non_coding_transcript_exon_variant | 1/20 | |||
BMP1 | NR_033404.2 | n.112C>T | non_coding_transcript_exon_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP1 | ENST00000306385.10 | c.78C>T | p.Ala26= | synonymous_variant | 1/20 | 1 | NM_006129.5 | P1 | |
BMP1 | ENST00000306349.13 | c.78C>T | p.Ala26= | synonymous_variant | 1/16 | 1 | NM_001199.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000186 AC: 4AN: 215456Hom.: 0 AF XY: 0.0000250 AC XY: 3AN XY: 119980
GnomAD4 exome AF: 0.00000417 AC: 6AN: 1438242Hom.: 0 Cov.: 32 AF XY: 0.00000699 AC XY: 5AN XY: 715570
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at