chr1-26123610-A-G

Position:

• chr1-26123610-A-G

Variant summary

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

The NM_152835.5(PDIK1L):​c.*1033A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,602 control chromosomes in the GnomAD database, including 2,268 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 (2267 hom., cov: 32)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: PDIK1L NM_152835.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDIK1L	NM_152835.5	c.*1033A>G		3_prime_UTR_variant	3/3	ENST00000374269.2	NP_690048.1
PDIK1L	NM_001243532.2	c.*1033A>G		3_prime_UTR_variant	3/3		NP_001230461.1
PDIK1L	NM_001243533.2	c.*1033A>G		3_prime_UTR_variant	4/4		NP_001230462.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDIK1L	ENST00000374269.2	c.*1033A>G		3_prime_UTR_variant	3/3	1	NM_152835.5	ENSP00000363387	P1
PDIK1L	ENST00000374271.8	c.*1033A>G		3_prime_UTR_variant	4/4	1		ENSP00000363389	P1
PDIK1L	ENST00000619836.4	c.*1033A>G		3_prime_UTR_variant	3/3	3		ENSP00000480635	P1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25181 AN: 152044 Hom.: 2268 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.177

GnomAD4 exome AF: 0.134 AC: 59 AN: 440 Hom.: 1 Cov.: 0 AF XY: 0.152 AC XY: 40 AN XY: 264

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.136

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.166 AC: 25185 AN: 152162 Hom.: 2267 Cov.: 32 AF XY: 0.160 AC XY: 11893 AN XY: 74386

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0661

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.178

Alfa AF: 0.174 Hom.: 2249

Bravo AF: 0.168

Asia WGS AF: 0.0640 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	11
DANN	Benign	0.86

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: rs17257120; hg19: chr1-26450101; COSMIC: COSV65323125; COSMIC: COSV65323125;