GeneBe

ENST00000478197.1:n.219+90920G>A

Variant names:

Variant summary

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

The ENST00000478197.1(C2orf88):​n.219+90920G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,120 control chromosomes in the GnomAD database, including 5,135 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 0.24 ( 5135 hom., cov: 32)

Consequence

C2orf88
ENST00000478197.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.192

Publications

6 publications found
Variant links:
Genes affected
C2orf88 (HGNC:28191): (chromosome 2 open reading frame 88) Predicted to enable protein kinase A regulatory subunit binding activity. Predicted to be located in plasma membrane. [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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AKAP19XM_047446008.1 linkc.-518+73184G>A intron_variant Intron 2 of 6 XP_047301964.1
AKAP19XM_047446009.1 linkc.-518+91069G>A intron_variant Intron 1 of 5 XP_047301965.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
C2orf88ENST00000478197.1 linkn.219+90920G>A intron_variant Intron 1 of 1 4
C2orf88ENST00000495546.1 linkn.201+90920G>A intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.238
AC:
36125
AN:
152002
Hom.:
5126
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.406
Gnomad AMI
AF:
0.0899
Gnomad AMR
AF:
0.166
Gnomad ASJ
AF:
0.231
Gnomad EAS
AF:
0.0998
Gnomad SAS
AF:
0.161
Gnomad FIN
AF:
0.157
Gnomad MID
AF:
0.294
Gnomad NFE
AF:
0.182
Gnomad OTH
AF:
0.237
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.238
AC:
36171
AN:
152120
Hom.:
5135
Cov.:
32
AF XY:
0.233
AC XY:
17317
AN XY:
74390
show subpopulations
African (AFR)
AF:
0.406
AC:
16815
AN:
41450
American (AMR)
AF:
0.166
AC:
2532
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.231
AC:
802
AN:
3472
East Asian (EAS)
AF:
0.0995
AC:
516
AN:
5186
South Asian (SAS)
AF:
0.161
AC:
774
AN:
4818
European-Finnish (FIN)
AF:
0.157
AC:
1664
AN:
10572
Middle Eastern (MID)
AF:
0.299
AC:
88
AN:
294
European-Non Finnish (NFE)
AF:
0.182
AC:
12393
AN:
68012
Other (OTH)
AF:
0.239
AC:
505
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1328
2657
3985
5314
6642
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
358
716
1074
1432
1790
<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:
0.202
Hom.:
11240
Bravo
AF:
0.247
Asia WGS
AF:
0.178
AC:
618
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.4
DANN
Benign
0.31
PhyloP100
0.19

Splicing

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

Publications

Other links and lift over

dbSNP: rs6749643; hg19: chr2-190835473; API