chr10-70646006-C-T

Variant names:

• chr10-70646006-C-T
• rs826460
• ENST00000697571.1:c.*18-21497C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000697571.1(PALD1):​c.*18-21497C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,882 control chromosomes in the GnomAD database, including 16,795 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 0.46 (16795 hom., cov: 31)
• Consequence: PALD1 ENST00000697571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALD1	ENST00000697571.1	c.*18-21497C>T		intron_variant	Intron 20 of 20			ENSP00000513342.1
PALD1	ENST00000697573.1	c.*18-21497C>T		intron_variant	Intron 19 of 19			ENSP00000513344.1
PALD1	ENST00000697572.1	c.2251-21373C>T		intron_variant	Intron 18 of 18			ENSP00000513343.1
PALD1	ENST00000697575.1	n.113-6306C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69987 AN: 151764 Hom.: 16787 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.459

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.461 AC: 70033 AN: 151882 Hom.: 16795 Cov.: 31 AF XY: 0.467 AC XY: 34660 AN XY: 74216

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.460

Alfa AF: 0.452 Hom.: 31114

Bravo AF: 0.467

Asia WGS AF: 0.591 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs826460; hg19: chr10-72405762;