3-195579418-A-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001647.4(APOD):āc.44T>Cā(p.Phe15Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00461 in 1,614,068 control chromosomes in the GnomAD database, including 31 homozygotes. 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 Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001647.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APOD | NM_001647.4 | c.44T>C | p.Phe15Ser | missense_variant | 2/5 | ENST00000343267.8 | NP_001638.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOD | ENST00000343267.8 | c.44T>C | p.Phe15Ser | missense_variant | 2/5 | 1 | NM_001647.4 | ENSP00000345179.3 |
Frequencies
GnomAD3 genomes AF: 0.00421 AC: 641AN: 152212Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00422 AC: 1056AN: 250390Hom.: 7 AF XY: 0.00451 AC XY: 611AN XY: 135542
GnomAD4 exome AF: 0.00465 AC: 6802AN: 1461738Hom.: 28 Cov.: 31 AF XY: 0.00455 AC XY: 3310AN XY: 727178
GnomAD4 genome AF: 0.00421 AC: 641AN: 152330Hom.: 3 Cov.: 33 AF XY: 0.00443 AC XY: 330AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 29, 2018 | - - |
APOD-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 04, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at