chr20-57171260-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001719.3(BMP7):c.1147-152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00326 in 1,124,550 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 50 hom., cov: 33)
Exomes 𝑓: 0.0015 ( 26 hom. )
Consequence
BMP7
NM_001719.3 intron
NM_001719.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.15
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 20-57171260-T-C is Benign according to our data. Variant chr20-57171260-T-C is described in ClinVar as [Benign]. Clinvar id is 1273116.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0145 (2212/152342) while in subpopulation AFR AF= 0.0503 (2089/41566). AF 95% confidence interval is 0.0485. There are 50 homozygotes in gnomad4. There are 1038 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2210 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP7 | NM_001719.3 | c.1147-152A>G | intron_variant | ENST00000395863.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP7 | ENST00000395863.8 | c.1147-152A>G | intron_variant | 1 | NM_001719.3 | P1 | |||
BMP7 | ENST00000395864.7 | c.949-152A>G | intron_variant | 5 | |||||
BMP7 | ENST00000460817.5 | n.647-152A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
BMP7 | ENST00000476877.1 | n.391-152A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0145 AC: 2210AN: 152224Hom.: 50 Cov.: 33
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GnomAD4 exome AF: 0.00150 AC: 1454AN: 972208Hom.: 26 AF XY: 0.00119 AC XY: 591AN XY: 495860
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at