chr1-178853707-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004673.4(ANGPTL1):c.904A>C(p.Asn302His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004673.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPTL1 | NM_004673.4 | c.904A>C | p.Asn302His | missense_variant | 4/6 | ENST00000234816.7 | |
RALGPS2 | NM_152663.5 | c.607+20157T>G | intron_variant | ENST00000367635.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL1 | ENST00000234816.7 | c.904A>C | p.Asn302His | missense_variant | 4/6 | 1 | NM_004673.4 | P1 | |
RALGPS2 | ENST00000367635.8 | c.607+20157T>G | intron_variant | 1 | NM_152663.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250388Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135406
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460672Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726692
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2023 | The c.904A>C (p.N302H) alteration is located in exon 4 (coding exon 2) of the ANGPTL1 gene. This alteration results from a A to C substitution at nucleotide position 904, causing the asparagine (N) at amino acid position 302 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at