chr20-57175004-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001719.3(BMP7):āc.962A>Gā(p.Asn321Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00363 in 1,610,820 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0034 ( 1 hom., cov: 33)
Exomes š: 0.0037 ( 43 hom. )
Consequence
BMP7
NM_001719.3 missense
NM_001719.3 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 3.76
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.00505054).
BP6
Variant 20-57175004-T-C is Benign according to our data. Variant chr20-57175004-T-C is described in ClinVar as [Benign]. Clinvar id is 771049.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-57175004-T-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00343 (523/152332) while in subpopulation SAS AF= 0.0203 (98/4832). AF 95% confidence interval is 0.017. There are 1 homozygotes in gnomad4. There are 279 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 523 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMP7 | NM_001719.3 | c.962A>G | p.Asn321Ser | missense_variant | 5/7 | ENST00000395863.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMP7 | ENST00000395863.8 | c.962A>G | p.Asn321Ser | missense_variant | 5/7 | 1 | NM_001719.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00344 AC: 524AN: 152214Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00537 AC: 1332AN: 248000Hom.: 14 AF XY: 0.00622 AC XY: 835AN XY: 134172
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GnomAD4 exome AF: 0.00365 AC: 5330AN: 1458488Hom.: 43 Cov.: 32 AF XY: 0.00411 AC XY: 2982AN XY: 725600
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GnomAD4 genome AF: 0.00343 AC: 523AN: 152332Hom.: 1 Cov.: 33 AF XY: 0.00375 AC XY: 279AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 27, 2023 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
BMP7-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 24, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Congenital total pulmonary venous return anomaly Benign:1
Benign, no assertion criteria provided | case-control | Cytogenetics- Mohapatra Lab, Banaras Hindu University | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Uncertain
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;T;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;B
Vest4
MVP
MPC
ClinPred
T
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at