19-49861227-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_007254.4(PNKP):​c.*21A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00721 in 1,489,272 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0048 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0075 ( 70 hom. )

Consequence

PNKP
NM_007254.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.03
Variant links:
Genes affected
PNKP (HGNC:9154): (polynucleotide kinase 3'-phosphatase) This locus represents a gene involved in DNA repair. In response to ionizing radiation or oxidative damage, the protein encoded by this locus catalyzes 5' phosphorylation and 3' dephosphorylation of nucleic acids. Mutations at this locus have been associated with microcephaly, seizures, and developmental delay.[provided by RefSeq, Sep 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 19-49861227-T-G is Benign according to our data. Variant chr19-49861227-T-G is described in ClinVar as [Benign]. Clinvar id is 329890.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00481 (733/152288) while in subpopulation SAS AF= 0.0155 (75/4830). AF 95% confidence interval is 0.0127. There are 1 homozygotes in gnomad4. There are 369 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 70 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PNKPNM_007254.4 linkuse as main transcriptc.*21A>C 3_prime_UTR_variant 17/17 ENST00000322344.8 NP_009185.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PNKPENST00000322344.8 linkuse as main transcriptc.*21A>C 3_prime_UTR_variant 17/171 NM_007254.4 ENSP00000323511 P1Q96T60-1

Frequencies

GnomAD3 genomes
AF:
0.00481
AC:
732
AN:
152170
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00145
Gnomad AMI
AF:
0.0143
Gnomad AMR
AF:
0.00340
Gnomad ASJ
AF:
0.00346
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.0153
Gnomad FIN
AF:
0.00415
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00690
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00661
AC:
1643
AN:
248644
Hom.:
12
AF XY:
0.00763
AC XY:
1031
AN XY:
135064
show subpopulations
Gnomad AFR exome
AF:
0.00160
Gnomad AMR exome
AF:
0.00321
Gnomad ASJ exome
AF:
0.00340
Gnomad EAS exome
AF:
0.000382
Gnomad SAS exome
AF:
0.0187
Gnomad FIN exome
AF:
0.00551
Gnomad NFE exome
AF:
0.00661
Gnomad OTH exome
AF:
0.00607
GnomAD4 exome
AF:
0.00748
AC:
10001
AN:
1336984
Hom.:
70
Cov.:
20
AF XY:
0.00785
AC XY:
5270
AN XY:
671666
show subpopulations
Gnomad4 AFR exome
AF:
0.00142
Gnomad4 AMR exome
AF:
0.00334
Gnomad4 ASJ exome
AF:
0.00322
Gnomad4 EAS exome
AF:
0.000128
Gnomad4 SAS exome
AF:
0.0186
Gnomad4 FIN exome
AF:
0.00520
Gnomad4 NFE exome
AF:
0.00749
Gnomad4 OTH exome
AF:
0.00676
GnomAD4 genome
AF:
0.00481
AC:
733
AN:
152288
Hom.:
1
Cov.:
32
AF XY:
0.00495
AC XY:
369
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.00144
Gnomad4 AMR
AF:
0.00340
Gnomad4 ASJ
AF:
0.00346
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.0155
Gnomad4 FIN
AF:
0.00415
Gnomad4 NFE
AF:
0.00690
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00302
Hom.:
0
Bravo
AF:
0.00457
Asia WGS
AF:
0.00375
AC:
13
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Microcephaly, seizures, and developmental delay Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
0.012
DANN
Benign
0.78

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201872477; hg19: chr19-50364484; API