10-70572684-T-C

Position:

• chr10-70572684-T-C

Variant summary

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

The ENST00000697571.1(PALD1):​c.2418+8165T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,090 control chromosomes in the GnomAD database, including 19,625 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 0.49 (19625 hom., cov: 32)
• Consequence: PALD1 ENST00000697571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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.2418+8165T>C		intron_variant
PALD1	ENST00000697572.1	c.2250+8165T>C		intron_variant
PALD1	ENST00000697573.1	c.2262+25238T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74386 AN: 151972 Hom.: 19612 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.489 AC: 74415 AN: 152090 Hom.: 19625 Cov.: 32 AF XY: 0.492 AC XY: 36598 AN XY: 74346

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.471

Alfa AF: 0.550 Hom.: 49152

Bravo AF: 0.462

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10999409; hg19: chr10-72332440;