rs75925789
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000697571.1(PALD1):c.*17+4347C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0168 in 152,296 control chromosomes in the GnomAD database, including 53 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 0.017 ( 53 hom., cov: 32)
Consequence
PALD1
ENST00000697571.1 intron
ENST00000697571.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.394
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0551 is higher than 0.05.
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+4347C>T | intron_variant | ||||||
PALD1 | ENST00000697572.1 | c.2250+38912C>T | intron_variant | ||||||
PALD1 | ENST00000697573.1 | c.*17+4347C>T | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0168 AC: 2556AN: 152178Hom.: 53 Cov.: 32
GnomAD3 genomes
?
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2556
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152178
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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: 0.0168 AC: 2563AN: 152296Hom.: 53 Cov.: 32 AF XY: 0.0167 AC XY: 1241AN XY: 74470
GnomAD4 genome
?
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AC:
2563
AN:
152296
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Cov.:
32
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AC XY:
1241
AN XY:
74470
Gnomad4 AFR
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5
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