chr20-57225881-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001719.3(BMP7):c.611+2348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 469,852 control chromosomes in the GnomAD database, including 38,352 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.36 ( 10532 hom., cov: 32)
Exomes 𝑓: 0.41 ( 27820 hom. )
Consequence
BMP7
NM_001719.3 intron
NM_001719.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.59
Genes affected
BMP7 (HGNC:1074): (bone morphogenetic protein 7) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer, which plays a role in bone, kidney and brown adipose tissue development. Additionally, this protein induces ectopic bone formation and may promote fracture healing in human patients. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP7 | NM_001719.3 | c.611+2348G>A | intron_variant | ENST00000395863.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP7 | ENST00000395863.8 | c.611+2348G>A | intron_variant | 1 | NM_001719.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.358 AC: 53980AN: 150944Hom.: 10528 Cov.: 32
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GnomAD3 exomes AF: 0.375 AC: 56266AN: 149882Hom.: 11748 AF XY: 0.385 AC XY: 30991AN XY: 80584
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GnomAD4 exome AF: 0.407 AC: 129870AN: 318788Hom.: 27820 Cov.: 0 AF XY: 0.413 AC XY: 74394AN XY: 180126
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GnomAD4 genome AF: 0.358 AC: 54021AN: 151064Hom.: 10532 Cov.: 32 AF XY: 0.361 AC XY: 26650AN XY: 73850
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at