dbSNP rs17257120: PDIK1L:c.*1033A>G (chr1-26123610-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21

Publications

8 publications found

Variant links:

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]

PDIK1L links:

ENSG00000309933 (HGNC:):

ENSG00000309933 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank	MANE	Protein	UniProt
PDIK1L	NM_152835.5 link	c.*1033A>G	3_prime_UTR_variant	Exon 3 of 3	ENST00000374269.2	NP_690048.1	Q8N165
PDIK1L	NM_001243532.2 link	c.*1033A>G	3_prime_UTR_variant	Exon 3 of 3		NP_001230461.1	Q8N165
PDIK1L	NM_001243533.2 link	c.*1033A>G	3_prime_UTR_variant	Exon 4 of 4		NP_001230462.1	Q8N165

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PDIK1L	ENST00000374269.2 link	c.*1033A>G	3_prime_UTR_variant	Exon 3 of 3	1	NM_152835.5	ENSP00000363387.1	Q8N165
PDIK1L	ENST00000374271.8 link	c.*1033A>G	3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000363389.4	Q8N165
PDIK1L	ENST00000619836.4 link	c.*1033A>G	3_prime_UTR_variant	Exon 3 of 3	3		ENSP00000480635.1	Q8N165
ENSG00000309933	ENST00000846013.1 link	n.89+2774T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25181

AN:

152044

Hom.:

2268

Cov.:

show subpopulations

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:

AN:

440

Hom.:

Cov.:

AF XY:

0.152

AC XY:

AN XY:

264

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.136

AC:

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.166

AC:

25185

AN:

152162

Hom.:

2267

Cov.:

AF XY:

0.160

AC XY:

11893

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.199

AC:

8280

AN:

41516

American (AMR)

AF:

0.133

AC:

2037

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.203

AC:

703

AN:

3468

East Asian (EAS)

AF:

0.0166

AC:

AN:

5188

South Asian (SAS)

AF:

0.0661

AC:

319

AN:

4826

European-Finnish (FIN)

AF:

0.147

AC:

1553

AN:

10590

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11599

AN:

67970

Other (OTH)

AF:

0.178

AC:

377

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1071

2142

3213

4284

5355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

272

544

816

1088

1360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.172

Hom.:

5655

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

(source)

DANN

Benign

0.86

PhyloP100

1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over