chr4-94910269-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001203.3(BMPR1B):​c.-113+34369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 151,990 control chromosomes in the GnomAD database, including 7,585 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 7585 hom., cov: 32)

Consequence

BMPR1B
NM_001203.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0610
Variant links:
Genes affected
BMPR1B (HGNC:1077): (bone morphogenetic protein receptor type 1B) This gene encodes a member of the bone morphogenetic protein (BMP) receptor family of transmembrane serine/threonine kinases. The ligands of this receptor are BMPs, which are members of the TGF-beta superfamily. BMPs are involved in endochondral bone formation and embryogenesis. These proteins transduce their signals through the formation of heteromeric complexes of 2 different types of serine (threonine) kinase receptors: type I receptors of about 50-55 kD and type II receptors of about 70-80 kD. Type II receptors bind ligands in the absence of type I receptors, but they require their respective type I receptors for signaling, whereas type I receptors require their respective type II receptors for ligand binding. Mutations in this gene have been associated with primary pulmonary hypertension. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BMPR1BNM_001203.3 linkuse as main transcriptc.-113+34369T>C intron_variant ENST00000515059.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BMPR1BENST00000515059.6 linkuse as main transcriptc.-113+34369T>C intron_variant 1 NM_001203.3 P4O00238-1

Frequencies

GnomAD3 genomes
AF:
0.280
AC:
42540
AN:
151872
Hom.:
7575
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.507
Gnomad AMI
AF:
0.156
Gnomad AMR
AF:
0.166
Gnomad ASJ
AF:
0.180
Gnomad EAS
AF:
0.0970
Gnomad SAS
AF:
0.227
Gnomad FIN
AF:
0.189
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.208
Gnomad OTH
AF:
0.244
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.280
AC:
42573
AN:
151990
Hom.:
7585
Cov.:
32
AF XY:
0.274
AC XY:
20340
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.506
Gnomad4 AMR
AF:
0.166
Gnomad4 ASJ
AF:
0.180
Gnomad4 EAS
AF:
0.0972
Gnomad4 SAS
AF:
0.226
Gnomad4 FIN
AF:
0.189
Gnomad4 NFE
AF:
0.208
Gnomad4 OTH
AF:
0.241
Alfa
AF:
0.255
Hom.:
754
Bravo
AF:
0.285
Asia WGS
AF:
0.162
AC:
563
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
1.6
DANN
Benign
0.56

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: rs2240036; hg19: chr4-95831420; API