GeneBe

NM_017915.5:c.1264-615G>A

Variant names:

Variant summary

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

The NM_017915.5(PARPBP):​c.1264-615G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,666 control chromosomes in the GnomAD database, including 1,776 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 0.15 ( 1776 hom., cov: 32)

Consequence

PARPBP
NM_017915.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.534

Publications

4 publications found
Variant links:
Genes affected
PARPBP (HGNC:26074): (PARP1 binding protein) Predicted to enable DNA binding activity. Involved in negative regulation of double-strand break repair via homologous recombination. Located in chromatin and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PARPBPNM_017915.5 linkc.1264-615G>A intron_variant Intron 9 of 10 ENST00000327680.7 NP_060385.3 Q9NWS1-1B4DT40

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PARPBPENST00000327680.7 linkc.1264-615G>A intron_variant Intron 9 of 10 2 NM_017915.5 ENSP00000332915.3 Q9NWS1-1

Frequencies

GnomAD3 genomes
AF:
0.148
AC:
22404
AN:
151546
Hom.:
1774
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.106
Gnomad AMI
AF:
0.0570
Gnomad AMR
AF:
0.0965
Gnomad ASJ
AF:
0.154
Gnomad EAS
AF:
0.125
Gnomad SAS
AF:
0.136
Gnomad FIN
AF:
0.206
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.179
Gnomad OTH
AF:
0.143
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.148
AC:
22420
AN:
151666
Hom.:
1776
Cov.:
32
AF XY:
0.147
AC XY:
10862
AN XY:
74098
show subpopulations
African (AFR)
AF:
0.106
AC:
4410
AN:
41462
American (AMR)
AF:
0.0964
AC:
1465
AN:
15198
Ashkenazi Jewish (ASJ)
AF:
0.154
AC:
534
AN:
3470
East Asian (EAS)
AF:
0.126
AC:
650
AN:
5172
South Asian (SAS)
AF:
0.137
AC:
660
AN:
4826
European-Finnish (FIN)
AF:
0.206
AC:
2169
AN:
10552
Middle Eastern (MID)
AF:
0.146
AC:
43
AN:
294
European-Non Finnish (NFE)
AF:
0.179
AC:
12132
AN:
67672
Other (OTH)
AF:
0.145
AC:
305
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
974
1948
2923
3897
4871
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
260
520
780
1040
1300
<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:
0.165
Hom.:
3787
Bravo
AF:
0.138
Asia WGS
AF:
0.146
AC:
507
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
1.9
DANN
Benign
0.73
PhyloP100
-0.53
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs11111201; hg19: chr12-102588475; API