rs719856
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012120.3(CD2AP):c.*2759G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,980 control chromosomes in the GnomAD database, including 5,505 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_012120.3 3_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- focal segmental glomerulosclerosis 3, susceptibility toInheritance: AD, AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- familial idiopathic steroid-resistant nephrotic syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD2AP | NM_012120.3 | c.*2759G>A | 3_prime_UTR_variant | Exon 18 of 18 | ENST00000359314.5 | NP_036252.1 | ||
CD2AP | XM_005248976.2 | c.*2759G>A | 3_prime_UTR_variant | Exon 18 of 18 | XP_005249033.1 | |||
CD2AP | XM_011514449.3 | c.*2759G>A | 3_prime_UTR_variant | Exon 17 of 17 | XP_011512751.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.251 AC: 37987AN: 151428Hom.: 5479 Cov.: 32 show subpopulations
GnomAD4 exome AF: 0.317 AC: 137AN: 432Hom.: 16 Cov.: 0 AF XY: 0.304 AC XY: 79AN XY: 260 show subpopulations
GnomAD4 genome AF: 0.251 AC: 38016AN: 151548Hom.: 5489 Cov.: 32 AF XY: 0.260 AC XY: 19288AN XY: 74050 show subpopulations
ClinVar
Submissions by phenotype
Focal segmental glomerulosclerosis 3, susceptibility to Benign:1
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