chr20-57175004-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001719.3(BMP7):ā€‹c.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

Scores

5
13

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 3.76
Variant links:
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
BMP7NM_001719.3 linkuse as main transcriptc.962A>G p.Asn321Ser missense_variant 5/7 ENST00000395863.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BMP7ENST00000395863.8 linkuse as main transcriptc.962A>G p.Asn321Ser missense_variant 5/71 NM_001719.3 P1

Frequencies

GnomAD3 genomes
AF:
0.00344
AC:
524
AN:
152214
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000772
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00844
Gnomad ASJ
AF:
0.0127
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0203
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.00279
Gnomad OTH
AF:
0.00861
GnomAD3 exomes
AF:
0.00537
AC:
1332
AN:
248000
Hom.:
14
AF XY:
0.00622
AC XY:
835
AN XY:
134172
show subpopulations
Gnomad AFR exome
AF:
0.000682
Gnomad AMR exome
AF:
0.00467
Gnomad ASJ exome
AF:
0.0153
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0190
Gnomad FIN exome
AF:
0.000305
Gnomad NFE exome
AF:
0.00327
Gnomad OTH exome
AF:
0.00870
GnomAD4 exome
AF:
0.00365
AC:
5330
AN:
1458488
Hom.:
43
Cov.:
32
AF XY:
0.00411
AC XY:
2982
AN XY:
725600
show subpopulations
Gnomad4 AFR exome
AF:
0.00114
Gnomad4 AMR exome
AF:
0.00481
Gnomad4 ASJ exome
AF:
0.0161
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0179
Gnomad4 FIN exome
AF:
0.000237
Gnomad4 NFE exome
AF:
0.00241
Gnomad4 OTH exome
AF:
0.00507
GnomAD4 genome
AF:
0.00343
AC:
523
AN:
152332
Hom.:
1
Cov.:
33
AF XY:
0.00375
AC XY:
279
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.000770
Gnomad4 AMR
AF:
0.00836
Gnomad4 ASJ
AF:
0.0127
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0203
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.00279
Gnomad4 OTH
AF:
0.00852
Alfa
AF:
0.00349
Hom.:
2
Bravo
AF:
0.00349
TwinsUK
AF:
0.00324
AC:
12
ALSPAC
AF:
0.00259
AC:
10
ESP6500AA
AF:
0.000681
AC:
3
ESP6500EA
AF:
0.00233
AC:
20
ExAC
AF:
0.00537
AC:
652
Asia WGS
AF:
0.00779
AC:
27
AN:
3478
EpiCase
AF:
0.00529
EpiControl
AF:
0.00517

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 27, 2023- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
BMP7-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMar 24, 2021This 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 providedcase-controlCytogenetics- Mohapatra Lab, Banaras Hindu University-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.087
BayesDel_addAF
Benign
-0.46
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
12
DANN
Benign
0.31
DEOGEN2
Uncertain
0.46
T;.;T
Eigen
Benign
-0.63
Eigen_PC
Benign
-0.49
FATHMM_MKL
Uncertain
0.77
D
LIST_S2
Uncertain
0.87
D;T;D
MetaRNN
Benign
0.0048
T;T;T
MetaSVM
Benign
-0.84
T
MutationAssessor
Uncertain
2.3
M;.;.
MutationTaster
Benign
1.0
D;D;N
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-0.87
N;N;N
REVEL
Benign
0.18
Sift
Benign
0.74
T;T;T
Sift4G
Benign
0.76
T;T;T
Polyphen
0.0
B;B;B
Vest4
0.20
MVP
0.73
MPC
0.54
ClinPred
0.0060
T
GERP RS
4.0
Varity_R
0.083
gMVP
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61733438; hg19: chr20-55750060; COSMIC: COSV67779412; COSMIC: COSV67779412; API