ENST00000316562.9:c.276G>A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The ENST00000316562.9(PANK2):c.276G>A(p.Arg92Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00707 in 1,575,564 control chromosomes in the GnomAD database, including 78 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R92R) has been classified as Likely benign.
Frequency
Consequence
ENST00000316562.9 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PANK2 | NM_001386393.1 | c.-55G>A | upstream_gene_variant | ENST00000610179.7 | NP_001373322.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00527 AC: 803AN: 152262Hom.: 18 Cov.: 33
GnomAD3 exomes AF: 0.00352 AC: 631AN: 179352Hom.: 2 AF XY: 0.00330 AC XY: 321AN XY: 97374
GnomAD4 exome AF: 0.00726 AC: 10334AN: 1423184Hom.: 60 Cov.: 31 AF XY: 0.00691 AC XY: 4869AN XY: 704950
GnomAD4 genome AF: 0.00527 AC: 803AN: 152380Hom.: 18 Cov.: 33 AF XY: 0.00491 AC XY: 366AN XY: 74516
ClinVar
Submissions by phenotype
not provided Benign:6
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2025 | PANK2: BP4, BP7, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 11, 2019 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 23, 2016 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 15, 2017 | - - |
Pigmentary pallidal degeneration Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2025 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at