chr3-9937570-G-C
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001077415.3(CRELD1):āc.266G>Cā(p.Arg89Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,458,264 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R89H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001077415.3 missense
Scores
Clinical Significance
Conservation
Publications
- complex neurodevelopmental disorderInheritance: AR Classification: STRONG Submitted by: Ambry Genetics
- atrioventricular septal defect, susceptibility to, 2Inheritance: AD Classification: MODERATE, LIMITED Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P
- Jeffries-Lakhani neurodevelopmental syndromeInheritance: AR Classification: MODERATE Submitted by: G2P
- congenital heart diseaseInheritance: AD Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRELD1 | NM_001077415.3 | c.266G>C | p.Arg89Pro | missense_variant | Exon 4 of 11 | ENST00000452070.6 | NP_001070883.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRELD1 | ENST00000452070.6 | c.266G>C | p.Arg89Pro | missense_variant | Exon 4 of 11 | 2 | NM_001077415.3 | ENSP00000393643.2 | ||
ENSG00000288550 | ENST00000683484.1 | n.*6G>C | non_coding_transcript_exon_variant | Exon 18 of 24 | ENSP00000507040.1 | |||||
ENSG00000288550 | ENST00000683484.1 | n.*6G>C | 3_prime_UTR_variant | Exon 18 of 24 | ENSP00000507040.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458264Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 725148 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at