rs2270004
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_152268.4(PARS2):c.704A>G(p.Asn235Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,613,830 control chromosomes in the GnomAD database, including 19,963 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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_152268.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARS2 | NM_152268.4 | c.704A>G | p.Asn235Ser | missense_variant | 2/2 | ENST00000371279.4 | NP_689481.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARS2 | ENST00000371279.4 | c.704A>G | p.Asn235Ser | missense_variant | 2/2 | 1 | NM_152268.4 | ENSP00000360327 | P1 |
Frequencies
GnomAD3 genomes AF: 0.153 AC: 23224AN: 151930Hom.: 1823 Cov.: 32
GnomAD3 exomes AF: 0.156 AC: 39201AN: 251262Hom.: 3284 AF XY: 0.160 AC XY: 21760AN XY: 135808
GnomAD4 exome AF: 0.155 AC: 227026AN: 1461782Hom.: 18138 Cov.: 34 AF XY: 0.157 AC XY: 113929AN XY: 727188
GnomAD4 genome AF: 0.153 AC: 23237AN: 152048Hom.: 1825 Cov.: 32 AF XY: 0.157 AC XY: 11657AN XY: 74334
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jul 31, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 25% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 23. Only high quality variants are reported. - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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 | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at