chr12-21848232-G-C
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_020297.4(ABCC9):c.2784C>G(p.Asp928Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,198 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_020297.4 missense
Scores
Clinical Significance
Conservation
Publications
- hypertrichotic osteochondrodysplasia Cantu typeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- dilated cardiomyopathy 1OInheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Illumina, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- intellectual disability and myopathy syndromeInheritance: AR Classification: MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- acromegaloid facial appearance syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial isolated dilated cardiomyopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hypertrichosis-acromegaloid facial appearance syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Brugada syndromeInheritance: AD Classification: LIMITED Submitted by: Genomics England PanelApp
- dilated cardiomyopathyInheritance: AD Classification: LIMITED Submitted by: ClinGen
- atrial fibrillation, familial, 12Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152084Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000637 AC: 16AN: 251212 AF XY: 0.0000368 show subpopulations
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461114Hom.: 0 Cov.: 31 AF XY: 0.0000482 AC XY: 35AN XY: 726862 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74288 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
The p.D928E variant (also known as c.2784C>G), located in coding exon 23 of the ABCC9 gene, results from a C to G substitution at nucleotide position 2784. The aspartic acid at codon 928 is replaced by glutamic acid, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Dilated cardiomyopathy 1O Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at