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GeneBe

rs75925789

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.394
Variant links:
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
PALD1ENST00000697571.1 linkuse as main transcriptc.*17+4347C>T intron_variant
PALD1ENST00000697572.1 linkuse as main transcriptc.2250+38912C>T intron_variant
PALD1ENST00000697573.1 linkuse as main transcriptc.*17+4347C>T intron_variant

Frequencies

GnomAD3 genomes
AF:
0.0168
AC:
2556
AN:
152178
Hom.:
53
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0570
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00798
Gnomad ASJ
AF:
0.00634
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000220
Gnomad OTH
AF:
0.0167
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0168
AC:
2563
AN:
152296
Hom.:
53
Cov.:
32
AF XY:
0.0167
AC XY:
1241
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.0570
Gnomad4 AMR
AF:
0.00797
Gnomad4 ASJ
AF:
0.00634
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000220
Gnomad4 OTH
AF:
0.0165
Alfa
AF:
0.0188
Hom.:
4
Bravo
AF:
0.0195
Asia WGS
AF:
0.00144
AC:
5
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
7.1
Dann
Benign
0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs75925789; hg19: chr10-72363187; API