10-70646006-C-T

Position:

• chr10-70646006-C-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PALD1	ENST00000697571.1	c.*18-21497C>T		intron_variant
PALD1	ENST00000697572.1	c.2251-21373C>T		intron_variant
PALD1	ENST00000697573.1	c.*18-21497C>T		intron_variant
PALD1	ENST00000697575.1	n.113-6306C>T		intron_variant, non_coding_transcript_variant

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;