rs2882676
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001369268.1(ACAN):āc.4523A>Cā(p.Glu1508Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 1,612,950 control chromosomes in the GnomAD database, including 297,361 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001369268.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACAN | NM_001369268.1 | c.4523A>C | p.Glu1508Ala | missense_variant | 12/19 | ENST00000560601.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACAN | ENST00000560601.4 | c.4523A>C | p.Glu1508Ala | missense_variant | 12/19 | 3 | NM_001369268.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.529 AC: 80012AN: 151262Hom.: 22317 Cov.: 31
GnomAD3 exomes AF: 0.525 AC: 130849AN: 249176Hom.: 37429 AF XY: 0.538 AC XY: 72778AN XY: 135202
GnomAD4 exome AF: 0.605 AC: 883519AN: 1461570Hom.: 275047 Cov.: 80 AF XY: 0.604 AC XY: 438969AN XY: 727070
GnomAD4 genome ? AF: 0.529 AC: 80019AN: 151380Hom.: 22314 Cov.: 31 AF XY: 0.521 AC XY: 38560AN XY: 73960
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 09, 2015 | - - |
Spondyloepimetaphyseal dysplasia, aggrecan type Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | This variant is associated with the following publications: (PMID: 17317784) - |
Osteochondritis dissecans Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Spondyloepiphyseal dysplasia, Kimberley type Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at