chr10-70603139-G-A

Variant names:

• chr10-70603139-G-A
• rs35069510
• ENST00000697571.1:c.*17+4055G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALD1	ENST00000697571.1	c.*17+4055G>A		intron_variant	Intron 20 of 20			ENSP00000513342.1
PALD1	ENST00000697573.1	c.*17+4055G>A		intron_variant	Intron 19 of 19			ENSP00000513344.1
PALD1	ENST00000697572.1	c.2250+38620G>A		intron_variant	Intron 18 of 18			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

African (AFR) AF: 0.0149 AC: 617 AN: 41524

American (AMR) AF: 0.0785 AC: 1199 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0602 AC: 209 AN: 3472

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5160

South Asian (SAS) AF: 0.00871 AC: 42 AN: 4824

European-Finnish (FIN) AF: 0.0319 AC: 339 AN: 10616

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0898 AC: 6107 AN: 67996

Other (OTH) AF: 0.0756 AC: 159 AN: 2104

Alfa AF: 0.0661 Hom.: 244

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
PhyloP100		1.1
PromoterAI		0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs35069510; hg19: chr10-72362895;