chr4-95104440-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001203.3(BMPR1B):c.16G>A(p.Ala6Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,613,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A6A) has been classified as Likely benign.
Frequency
Consequence
NM_001203.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMPR1B | NM_001203.3 | c.16G>A | p.Ala6Thr | missense_variant | 4/13 | ENST00000515059.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMPR1B | ENST00000515059.6 | c.16G>A | p.Ala6Thr | missense_variant | 4/13 | 1 | NM_001203.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 151988Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250864Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135594
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461160Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726864
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74330
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.16G>A (p.A6T) alteration is located in exon 4 (coding exon 1) of the BMPR1B gene. This alteration results from a G to A substitution at nucleotide position 16, causing the alanine (A) at amino acid position 6 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Type A2 brachydactyly;C4225404:Acromesomelic dysplasia 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at