rs35401316
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000697571.1(PALD1):c.*17+5005T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0156 in 152,316 control chromosomes in the GnomAD database, including 31 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 0.016 ( 31 hom., cov: 32)
Consequence
PALD1
ENST00000697571.1 intron
ENST00000697571.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.399
Genes affected
PALD1 (HGNC:23530): (phosphatase domain containing paladin 1) Predicted to enable protein tyrosine phosphatase activity. Predicted to be involved in peptidyl-tyrosine dephosphorylation. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.87).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0156 (2369/152316) while in subpopulation NFE AF= 0.0216 (1471/68018). AF 95% confidence interval is 0.0207. There are 31 homozygotes in gnomad4. There are 1240 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 31 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALD1 | ENST00000697571.1 | c.*17+5005T>C | intron_variant | ||||||
PALD1 | ENST00000697572.1 | c.2250+39570T>C | intron_variant | ||||||
PALD1 | ENST00000697573.1 | c.*17+5005T>C | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0156 AC: 2371AN: 152198Hom.: 31 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
2371
AN:
152198
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Cov.:
32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0156 AC: 2369AN: 152316Hom.: 31 Cov.: 32 AF XY: 0.0167 AC XY: 1240AN XY: 74474
GnomAD4 genome
?
AF:
AC:
2369
AN:
152316
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32
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1240
AN XY:
74474
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6
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at