rs144030074
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001365308.1(BMPER):āc.220A>Gā(p.Asn74Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00255 in 1,613,806 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001365308.1 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BMPER | NM_001365308.1 | c.220A>G | p.Asn74Asp | missense_variant, splice_region_variant | 3/15 | ENST00000649409.2 | |
BMPER | NM_133468.5 | c.220A>G | p.Asn74Asp | missense_variant, splice_region_variant | 4/16 | ||
BMPER | NM_001410872.1 | c.220A>G | p.Asn74Asp | missense_variant, splice_region_variant | 3/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BMPER | ENST00000649409.2 | c.220A>G | p.Asn74Asp | missense_variant, splice_region_variant | 3/15 | NM_001365308.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00146 AC: 222AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00175 AC: 440AN: 251354Hom.: 2 AF XY: 0.00197 AC XY: 268AN XY: 135840
GnomAD4 exome AF: 0.00267 AC: 3899AN: 1461512Hom.: 9 Cov.: 31 AF XY: 0.00262 AC XY: 1904AN XY: 727102
GnomAD4 genome ? AF: 0.00146 AC: 222AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.00118 AC XY: 88AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ExAC frequency. Not reported. Next to splice junction and LOF variants in gene are associated with autosomal recessive diaphanospondylodysostosis. - |
Diaphanospondylodysostosis Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at