rs2305778
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001370095.3(PODNL1):c.768-19C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0699 in 1,533,248 control chromosomes in the GnomAD database, including 4,235 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 0.056 ( 304 hom., cov: 33)
Exomes 𝑓: 0.071 ( 3931 hom. )
Consequence
PODNL1
NM_001370095.3 intron
NM_001370095.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.219
Genes affected
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PODNL1 | NM_001370095.3 | c.768-19C>T | intron_variant | ENST00000588872.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PODNL1 | ENST00000588872.3 | c.768-19C>T | intron_variant | 3 | NM_001370095.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0561 AC: 8530AN: 152116Hom.: 304 Cov.: 33
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GnomAD3 exomes AF: 0.0772 AC: 14611AN: 189162Hom.: 680 AF XY: 0.0818 AC XY: 8384AN XY: 102512
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GnomAD4 exome AF: 0.0715 AC: 98690AN: 1381014Hom.: 3931 Cov.: 31 AF XY: 0.0735 AC XY: 49899AN XY: 678834
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GnomAD4 genome ? AF: 0.0560 AC: 8530AN: 152234Hom.: 304 Cov.: 33 AF XY: 0.0582 AC XY: 4330AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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