10-86876022-C-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_004329.3(BMPR1A):c.4C>A(p.Pro2Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 1,592,936 control chromosomes in the GnomAD database, including 83,045 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004329.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.404 AC: 61375AN: 151904Hom.: 14968 Cov.: 32
GnomAD3 exomes AF: 0.358 AC: 89783AN: 251114Hom.: 18858 AF XY: 0.343 AC XY: 46507AN XY: 135738
GnomAD4 exome AF: 0.286 AC: 411907AN: 1440912Hom.: 68024 Cov.: 31 AF XY: 0.285 AC XY: 204519AN XY: 717892
GnomAD4 genome AF: 0.404 AC: 61474AN: 152024Hom.: 15021 Cov.: 32 AF XY: 0.408 AC XY: 30351AN XY: 74304
ClinVar
Submissions by phenotype
not specified Benign:5Other:1
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not provided Uncertain:1Benign:4
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This variant is associated with the following publications: (PMID: 24728327) -
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Juvenile polyposis syndrome Benign:4
This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. -
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Hereditary cancer-predisposing syndrome Benign:2
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This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Generalized juvenile polyposis/juvenile polyposis coli Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at