chr20-57183506-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001719.3(BMP7):​c.958+216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0619 in 152,162 control chromosomes in the GnomAD database, including 465 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.062 ( 465 hom., cov: 33)

Consequence

BMP7
NM_001719.3 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.154
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 -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 20-57183506-C-T is Benign according to our data. Variant chr20-57183506-C-T is described in ClinVar as [Benign]. Clinvar id is 1291873.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BMP7NM_001719.3 linkuse as main transcriptc.958+216G>A intron_variant ENST00000395863.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BMP7ENST00000395863.8 linkuse as main transcriptc.958+216G>A intron_variant 1 NM_001719.3 P1

Frequencies

GnomAD3 genomes
AF:
0.0618
AC:
9402
AN:
152044
Hom.:
463
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.130
Gnomad AMI
AF:
0.0899
Gnomad AMR
AF:
0.0312
Gnomad ASJ
AF:
0.0115
Gnomad EAS
AF:
0.0283
Gnomad SAS
AF:
0.0130
Gnomad FIN
AF:
0.0502
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0378
Gnomad OTH
AF:
0.0484
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0619
AC:
9424
AN:
152162
Hom.:
465
Cov.:
33
AF XY:
0.0608
AC XY:
4522
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.130
Gnomad4 AMR
AF:
0.0311
Gnomad4 ASJ
AF:
0.0115
Gnomad4 EAS
AF:
0.0284
Gnomad4 SAS
AF:
0.0124
Gnomad4 FIN
AF:
0.0502
Gnomad4 NFE
AF:
0.0377
Gnomad4 OTH
AF:
0.0503
Alfa
AF:
0.0499
Hom.:
58
Bravo
AF:
0.0639
Asia WGS
AF:
0.0480
AC:
165
AN:
3478

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 submitterclinical testingGeneDxAug 03, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.2
DANN
Benign
0.59

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: rs76737492; hg19: chr20-55758562; API