10-86875999-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004329.3(BMPR1A):c.-20G>A variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.0000107 in 1,584,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_004329.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251222Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135788
GnomAD4 exome AF: 0.00000558 AC: 8AN: 1432638Hom.: 0 Cov.: 27 AF XY: 0.00000280 AC XY: 2AN XY: 714682
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74480
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant is denoted BMPR1A c.-20G>A, and describes a nucleotide substitution 20 base pairs upstream of the BMPR1A ATG translational start site in the 5' untranslated region (UTR). This variant has not, to our knowledge, been published in the literature as being pathogenic or benign. The surrounding sequence, with the base that is substituted in brackets, is CACA[G/A]GAAA. This variant was observed at an allele frequency of 0.019% (2/10,372) in individuals of African ancestry in large population cohorts (NHLBI Exome Sequencing Project, The 1000 Genomes Consortium 2015, Lek 2016). The guanine (G) nucleotide that is altered is conserved across species. At this time, we consider BMPR1A c.-20G>A to be a variant of uncertain significance. -
Hereditary cancer-predisposing syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at