1-178864964-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004673.4(ANGPTL1):c.813C>G(p.Phe271Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000241 in 1,449,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPTL1 | NM_004673.4 | c.813C>G | p.Phe271Leu | missense_variant | 3/6 | ENST00000234816.7 | |
RALGPS2 | NM_152663.5 | c.608-12534G>C | intron_variant | ENST00000367635.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL1 | ENST00000234816.7 | c.813C>G | p.Phe271Leu | missense_variant | 3/6 | 1 | NM_004673.4 | P1 | |
RALGPS2 | ENST00000367635.8 | c.608-12534G>C | intron_variant | 1 | NM_152663.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000371 AC: 6AN: 161892Hom.: 0 AF XY: 0.0000700 AC XY: 6AN XY: 85754
GnomAD4 exome AF: 0.0000262 AC: 34AN: 1297642Hom.: 0 Cov.: 30 AF XY: 0.0000286 AC XY: 18AN XY: 628624
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.813C>G (p.F271L) alteration is located in exon 3 (coding exon 1) of the ANGPTL1 gene. This alteration results from a C to G substitution at nucleotide position 813, causing the phenylalanine (F) at amino acid position 271 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