rs4714003
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NR_109836.1(PANDAR):n.644G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 1,527,664 control chromosomes in the GnomAD database, including 6 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 0.0015 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 3 hom. )
Consequence
PANDAR
NR_109836.1 non_coding_transcript_exon
NR_109836.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.386
Genes affected
LAP3P2 (HGNC:42365): (leucine aminopeptidase 3 pseudogene 2)
PANDAR (HGNC:44048): (promoter of CDKN1A antisense DNA damage activated RNA) This gene produces a non-coding RNA that is thought to regulate the response to DNA damage. This gene is induced by tumor protein p53 and interacts with and modulates the activity of a transcription factor that induce pro-apoptotic genes. Deregulation of this gene is associated with cancer progression. [provided by RefSeq, Dec 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BS2
?
High Homozygotes in GnomAd4 at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PANDAR | NR_109836.1 | n.644G>T | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAP3P2 | ENST00000454686.1 | n.667C>A | non_coding_transcript_exon_variant | 1/1 | |||||
PANDAR | ENST00000629595.1 | n.644G>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.00151 AC: 230AN: 152002Hom.: 3 Cov.: 32
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GnomAD4 exome AF: 0.00157 AC: 2159AN: 1375544Hom.: 3 Cov.: 26 AF XY: 0.00157 AC XY: 1079AN XY: 688868
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GnomAD4 genome ? AF: 0.00151 AC: 230AN: 152120Hom.: 3 Cov.: 32 AF XY: 0.00149 AC XY: 111AN XY: 74384
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at