GeneBe

chr13-18960017-C-T

Variant names:

Variant summary

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

The variant allele was found at a frequency of 0.302 in 186,646 control chromosomes in the GnomAD database, including 9,532 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 0.30 ( 7736 hom., cov: 33)
Exomes 𝑓: 0.29 ( 1796 hom. )

Consequence

PHF2P2
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0860

Publications

2 publications found
Variant links:
Genes affected
PHF2P2 (HGNC:38808): (PHD finger protein 2 pseudogene 2)

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=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PHF2P2 n.18960017C>T intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PHF2P2ENST00000444553.6 linkn.1594+79G>A intron_variant Intron 12 of 19 6

Frequencies

GnomAD3 genomes
AF:
0.304
AC:
46232
AN:
151952
Hom.:
7721
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.285
Gnomad AMI
AF:
0.218
Gnomad AMR
AF:
0.466
Gnomad ASJ
AF:
0.195
Gnomad EAS
AF:
0.627
Gnomad SAS
AF:
0.296
Gnomad FIN
AF:
0.289
Gnomad MID
AF:
0.210
Gnomad NFE
AF:
0.266
Gnomad OTH
AF:
0.286
GnomAD4 exome
AF:
0.291
AC:
10055
AN:
34576
Hom.:
1796
AF XY:
0.292
AC XY:
5269
AN XY:
18074
show subpopulations
African (AFR)
AF:
0.259
AC:
464
AN:
1792
American (AMR)
AF:
0.517
AC:
1363
AN:
2634
Ashkenazi Jewish (ASJ)
AF:
0.169
AC:
162
AN:
960
East Asian (EAS)
AF:
0.622
AC:
1213
AN:
1950
South Asian (SAS)
AF:
0.256
AC:
839
AN:
3272
European-Finnish (FIN)
AF:
0.252
AC:
267
AN:
1058
Middle Eastern (MID)
AF:
0.192
AC:
23
AN:
120
European-Non Finnish (NFE)
AF:
0.248
AC:
5162
AN:
20800
Other (OTH)
AF:
0.282
AC:
562
AN:
1990
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
318
637
955
1274
1592
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
84
168
252
336
420
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.304
AC:
46280
AN:
152070
Hom.:
7736
Cov.:
33
AF XY:
0.311
AC XY:
23103
AN XY:
74312
show subpopulations
African (AFR)
AF:
0.285
AC:
11829
AN:
41492
American (AMR)
AF:
0.467
AC:
7138
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
0.195
AC:
678
AN:
3472
East Asian (EAS)
AF:
0.628
AC:
3222
AN:
5128
South Asian (SAS)
AF:
0.295
AC:
1422
AN:
4814
European-Finnish (FIN)
AF:
0.289
AC:
3062
AN:
10594
Middle Eastern (MID)
AF:
0.212
AC:
62
AN:
292
European-Non Finnish (NFE)
AF:
0.266
AC:
18060
AN:
67970
Other (OTH)
AF:
0.288
AC:
609
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1609
3219
4828
6438
8047
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
472
944
1416
1888
2360
<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:
0.271
Hom.:
992
Bravo
AF:
0.320
Asia WGS
AF:
0.423
AC:
1469
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.22
DANN
Benign
0.58
PhyloP100
0.086

Splicing

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

Publications

Other links and lift over

dbSNP: rs1867248; hg19: chr13-19534157; API