1-178853745-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004673.4(ANGPTL1):c.866C>T(p.Ser289Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000181 in 1,602,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S289W) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPTL1 | NM_004673.4 | c.866C>T | p.Ser289Leu | missense_variant | 4/6 | ENST00000234816.7 | |
RALGPS2 | NM_152663.5 | c.607+20195G>A | intron_variant | ENST00000367635.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL1 | ENST00000234816.7 | c.866C>T | p.Ser289Leu | missense_variant | 4/6 | 1 | NM_004673.4 | P1 | |
RALGPS2 | ENST00000367635.8 | c.607+20195G>A | intron_variant | 1 | NM_152663.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152004Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000251 AC: 6AN: 239328Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 129782
GnomAD4 exome AF: 0.0000179 AC: 26AN: 1450474Hom.: 0 Cov.: 30 AF XY: 0.0000166 AC XY: 12AN XY: 721432
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152004Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74242
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.866C>T (p.S289L) alteration is located in exon 4 (coding exon 2) of the ANGPTL1 gene. This alteration results from a C to T substitution at nucleotide position 866, causing the serine (S) at amino acid position 289 to be replaced by a leucine (L). 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