rs142832849
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_153638.4(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 (★★).
Frequency
Consequence
NM_153638.4 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
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PANK2: BP4, BP7, BS2 -
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not specified Benign:2
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Pigmentary pallidal degeneration Benign:2
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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