chr2-69013519-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032208.3(ANTXR1):c.20G>A(p.Arg7Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,588,742 control chromosomes in the GnomAD database, including 650 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_032208.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANTXR1 | NM_032208.3 | c.20G>A | p.Arg7Lys | missense_variant | 1/18 | ENST00000303714.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANTXR1 | ENST00000303714.9 | c.20G>A | p.Arg7Lys | missense_variant | 1/18 | 1 | NM_032208.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1742AN: 152222Hom.: 51 Cov.: 32
GnomAD3 exomes AF: 0.0245 AC: 5024AN: 205318Hom.: 191 AF XY: 0.0242 AC XY: 2666AN XY: 110204
GnomAD4 exome AF: 0.0106 AC: 15160AN: 1436402Hom.: 599 Cov.: 31 AF XY: 0.0114 AC XY: 8115AN XY: 711692
GnomAD4 genome ? AF: 0.0114 AC: 1744AN: 152340Hom.: 51 Cov.: 32 AF XY: 0.0148 AC XY: 1103AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
ANTXR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2020 | 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