ENST00000697571.1:c.*17+4956T>C

Variant names:

• chr10-70604040-T-C
• rs10999428
• ENST00000697571.1:c.*17+4956T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000697571.1(PALD1):​c.*17+4956T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,276 control chromosomes in the GnomAD database, including 1,643 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 0.10 (1643 hom., cov: 32)
• Consequence: PALD1 ENST00000697571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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+4956T>C		intron_variant	Intron 20 of 20			ENSP00000513342.1
PALD1	ENST00000697573.1	c.*17+4956T>C		intron_variant	Intron 19 of 19			ENSP00000513344.1
PALD1	ENST00000697572.1	c.2250+39521T>C		intron_variant	Intron 18 of 18			ENSP00000513343.1

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15337 AN: 152158 Hom.: 1639 Cov.: 32

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.101 AC: 15352 AN: 152276 Hom.: 1643 Cov.: 32 AF XY: 0.107 AC XY: 8001 AN XY: 74448

African (AFR) AF: 0.0543 AC: 2257 AN: 41558

American (AMR) AF: 0.231 AC: 3533 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0654 AC: 227 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2887 AN: 5172

South Asian (SAS) AF: 0.171 AC: 827 AN: 4828

European-Finnish (FIN) AF: 0.0791 AC: 839 AN: 10608

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.0657 AC: 4467 AN: 68022

Other (OTH) AF: 0.112 AC: 237 AN: 2114

Alfa AF: 0.0942 Hom.: 633

Bravo AF: 0.116

Asia WGS AF: 0.293 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10999428; hg19: chr10-72363796;