10-70603139-G-A

Position:

• chr10-70603139-G-A

Variant summary

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

The ENST00000697571.1(PALD1):​c.*17+4055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0583 in 152,182 control chromosomes in the GnomAD database, including 364 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 0.058 (364 hom., cov: 31)
• Consequence: PALD1 ENST00000697571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.70603139G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PALD1	ENST00000697571.1	c.*17+4055G>A		intron_variant				ENSP00000513342.1
PALD1	ENST00000697573.1	c.*17+4055G>A		intron_variant				ENSP00000513344.1
PALD1	ENST00000697572.1	c.2250+38620G>A		intron_variant				ENSP00000513343.1

Frequencies

GnomAD3 genomes AF: 0.0583 AC: 8863 AN: 152064 Hom.: 364 Cov.: 31

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.0319

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.0759

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

GnomAD4 genome AF: 0.0583 AC: 8868 AN: 152182 Hom.: 364 Cov.: 31 AF XY: 0.0555 AC XY: 4128 AN XY: 74406

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.0785

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.00871

Gnomad4 FIN AF: 0.0319

Gnomad4 NFE AF: 0.0898

Gnomad4 OTH AF: 0.0756

Alfa AF: 0.0766 Hom.: 84

Bravo AF: 0.0608

Asia WGS AF: 0.00693 AC: 25 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35069510; hg19: chr10-72362895;