rs17257113

chr1-26123104-G-A

Variant summary

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

The NM_152835.5(PDIK1L):c.*527G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 151,850 control chromosomes in the GnomAD database, including 2,261 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 0.17 (2260 hom., cov: 31)
  • Exomes 𝑓: 0.14 (1 hom.)
• Consequence: PDIK1L NM_152835.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78

Genes affected

PDIK1L (HGNC:18981): (PDLIM1 interacting kinase 1 like) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in meiotic cell cycle. Located in nucleoplasm. [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=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDIK1L	NM_152835.5	c.*527G>A		3_prime_UTR_variant	3/3	ENST00000374269.2
PDIK1L	NM_001243532.2	c.*527G>A		3_prime_UTR_variant	3/3
PDIK1L	NM_001243533.2	c.*527G>A		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDIK1L	ENST00000374269.2	c.*527G>A		3_prime_UTR_variant	3/3	1	NM_152835.5	P1
PDIK1L	ENST00000374271.8	c.*527G>A		3_prime_UTR_variant	4/4	1		P1
PDIK1L	ENST00000619836.4	c.*527G>A		3_prime_UTR_variant	3/3	3		P1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25141 AN: 151324 Hom.: 2261 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.0676

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.177

GnomAD4 exome AF: 0.136 AC: 60 AN: 442 Hom.: 1 Cov.: 0 AF XY: 0.152 AC XY: 40 AN XY: 264

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.136

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.166 AC: 25145 AN: 151408 Hom.: 2260 Cov.: 31 AF XY: 0.161 AC XY: 11882 AN XY: 73926

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0167

Gnomad4 SAS AF: 0.0667

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.178

Alfa AF: 0.172 Hom.: 791

Bravo AF: 0.168

Asia WGS AF: 0.0640 AC: 222 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	12
Dann	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17257113; hg19: chr1-26449595;