14-53949883-CTTTTTTTTTTT-CTTTTTTTTTTTTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001202.6(BMP4):​c.*145_*148dupAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00031 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00058 ( 0 hom. )

Consequence

BMP4
NM_001202.6 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.04
Variant links:
Genes affected
BMP4 (HGNC:1071): (bone morphogenetic protein 4) 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. This protein regulates heart development and adipogenesis. Mutations in this gene are associated with orofacial cleft and microphthalmia in human patients. The encoded protein may also be involved in the pathology of multiple cardiovascular diseases and human cancers. [provided by RefSeq, Jul 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000305 (41/134398) while in subpopulation AFR AF= 0.00095 (32/33668). AF 95% confidence interval is 0.000691. There are 0 homozygotes in gnomad4. There are 17 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 41 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BMP4NM_001202.6 linkc.*145_*148dupAAAA 3_prime_UTR_variant Exon 4 of 4 ENST00000245451.9 NP_001193.2 P12644Q53XC5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BMP4ENST00000245451 linkc.*145_*148dupAAAA 3_prime_UTR_variant Exon 4 of 4 1 NM_001202.6 ENSP00000245451.4 P12644
BMP4ENST00000558984 linkc.*145_*148dupAAAA 3_prime_UTR_variant Exon 3 of 3 1 ENSP00000454134.1 P12644
BMP4ENST00000559087 linkc.*145_*148dupAAAA 3_prime_UTR_variant Exon 4 of 4 1 ENSP00000453485.1 P12644
BMP4ENST00000417573 linkc.*145_*148dupAAAA 3_prime_UTR_variant Exon 4 of 4 5 ENSP00000394165.1 P12644

Frequencies

GnomAD3 genomes
AF:
0.000305
AC:
41
AN:
134404
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000952
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000304
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000118
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000618
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000579
AC:
295
AN:
509686
Hom.:
0
Cov.:
0
AF XY:
0.000516
AC XY:
133
AN XY:
257742
show subpopulations
Gnomad4 AFR exome
AF:
0.00694
Gnomad4 AMR exome
AF:
0.000934
Gnomad4 ASJ exome
AF:
0.000807
Gnomad4 EAS exome
AF:
0.0000347
Gnomad4 SAS exome
AF:
0.000136
Gnomad4 FIN exome
AF:
0.000403
Gnomad4 NFE exome
AF:
0.000413
Gnomad4 OTH exome
AF:
0.000725
GnomAD4 genome
AF:
0.000305
AC:
41
AN:
134398
Hom.:
0
Cov.:
0
AF XY:
0.000263
AC XY:
17
AN XY:
64692
show subpopulations
Gnomad4 AFR
AF:
0.000950
Gnomad4 AMR
AF:
0.000304
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000118
Gnomad4 NFE
AF:
0.0000618
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs1555339771; hg19: chr14-54416601; API