rs3824603
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_148977.3(PANK1):c.*556C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,376 control chromosomes in the GnomAD database, including 4,924 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.24 ( 4908 hom., cov: 32)
Exomes 𝑓: 0.28 ( 16 hom. )
Consequence
PANK1
NM_148977.3 3_prime_UTR
NM_148977.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.271
Genes affected
PANK1 (HGNC:8598): (pantothenate kinase 1) This gene encodes a member of the pantothenate kinase family. Pantothenate kinases are key regulatory enzymes in the biosynthesis of coenzyme A (CoA). The encoded protein catalyzes the first and rate-limiting enzymatic reaction in CoA biosynthesis and is regulated by CoA through feedback inhibition. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. This gene and an intronic miRNA on the same strand are co-regulated by the tumor suppressor p53 (see PMID 20833636). [provided by RefSeq, Apr 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PANK1 | NM_148977.3 | c.*556C>T | 3_prime_UTR_variant | 7/7 | ENST00000307534.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PANK1 | ENST00000307534.10 | c.*556C>T | 3_prime_UTR_variant | 7/7 | 1 | NM_148977.3 | |||
PANK1 | ENST00000322191.10 | c.*556C>T | 3_prime_UTR_variant | 6/6 | 1 | ||||
PANK1 | ENST00000342512.4 | c.*556C>T | 3_prime_UTR_variant | 7/7 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.243 AC: 36891AN: 151844Hom.: 4900 Cov.: 32
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GnomAD4 exome AF: 0.280 AC: 116AN: 414Hom.: 16 Cov.: 0 AF XY: 0.288 AC XY: 72AN XY: 250
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GnomAD4 genome ? AF: 0.243 AC: 36904AN: 151962Hom.: 4908 Cov.: 32 AF XY: 0.247 AC XY: 18361AN XY: 74258
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at