rs35401316

Variant names:

• chr10-70604089-T-C
• rs35401316
• ENST00000697571.1:c.*17+5005T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000697571.1(PALD1):​c.*17+5005T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0156 in 152,316 control chromosomes in the GnomAD database, including 31 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 0.016 (31 hom., cov: 32)
• Consequence: PALD1 ENST00000697571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399
• Publications: 3 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=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0156 (2369/152316) while in subpopulation NFE AF = 0.0216 (1471/68018). AF 95% confidence interval is 0.0207. There are 31 homozygotes in GnomAd4. There are 1240 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 31 AR gene

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+5005T>C		intron_variant	Intron 20 of 20			ENSP00000513342.1
PALD1	ENST00000697573.1	c.*17+5005T>C		intron_variant	Intron 19 of 19			ENSP00000513344.1
PALD1	ENST00000697572.1	c.2250+39570T>C		intron_variant	Intron 18 of 18			ENSP00000513343.1

Frequencies

GnomAD3 genomes AF: 0.0156 AC: 2371 AN: 152198 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.00369

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0120

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0156 AC: 2369 AN: 152316 Hom.: 31 Cov.: 32 AF XY: 0.0167 AC XY: 1240 AN XY: 74474

African (AFR) AF: 0.00368 AC: 153 AN: 41576

American (AMR) AF: 0.0119 AC: 182 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00403 AC: 14 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00394 AC: 19 AN: 4820

European-Finnish (FIN) AF: 0.0458 AC: 487 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0216 AC: 1471 AN: 68018

Other (OTH) AF: 0.0152 AC: 32 AN: 2110

Alfa AF: 0.0196 Hom.: 6

Bravo AF: 0.0124

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.64
DANN	Benign	0.35
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs35401316; hg19: chr10-72363845;