GeneBe

2-189940936-A-G

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+61109A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,136 control chromosomes in the GnomAD database, including 3,096 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 0.20 ( 3096 hom., cov: 32)

Consequence

C2orf88
ENST00000478197.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.221

Publications

11 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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AKAP19XM_047446008.1 linkc.-518+43373A>G intron_variant Intron 2 of 6 XP_047301964.1
AKAP19XM_047446009.1 linkc.-518+61258A>G 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+61109A>G intron_variant Intron 1 of 1 4
C2orf88ENST00000495546.1 linkn.201+61109A>G intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.197
AC:
30019
AN:
152018
Hom.:
3093
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.267
Gnomad AMI
AF:
0.0899
Gnomad AMR
AF:
0.147
Gnomad ASJ
AF:
0.232
Gnomad EAS
AF:
0.106
Gnomad SAS
AF:
0.160
Gnomad FIN
AF:
0.157
Gnomad MID
AF:
0.263
Gnomad NFE
AF:
0.182
Gnomad OTH
AF:
0.203
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.198
AC:
30055
AN:
152136
Hom.:
3096
Cov.:
32
AF XY:
0.194
AC XY:
14467
AN XY:
74400
show subpopulations
African (AFR)
AF:
0.267
AC:
11076
AN:
41480
American (AMR)
AF:
0.147
AC:
2244
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.232
AC:
805
AN:
3466
East Asian (EAS)
AF:
0.106
AC:
547
AN:
5174
South Asian (SAS)
AF:
0.160
AC:
771
AN:
4830
European-Finnish (FIN)
AF:
0.157
AC:
1662
AN:
10578
Middle Eastern (MID)
AF:
0.265
AC:
78
AN:
294
European-Non Finnish (NFE)
AF:
0.182
AC:
12354
AN:
67996
Other (OTH)
AF:
0.206
AC:
436
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1230
2460
3691
4921
6151
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
320
640
960
1280
1600
<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:
0.187
Hom.:
10883
Bravo
AF:
0.201
Asia WGS
AF:
0.170
AC:
592
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
6.4
DANN
Benign
0.63
PhyloP100
0.22

Splicing

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

Publications

Other links and lift over

dbSNP: rs7571613; hg19: chr2-190805662; API