GeneBe

2-189947246-T-C

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+67419T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,156 control chromosomes in the GnomAD database, including 2,465 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 0.18 ( 2465 hom., cov: 33)

Consequence

C2orf88
ENST00000478197.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0940

Publications

5 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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AKAP19XM_047446008.1 linkc.-518+49683T>C intron_variant Intron 2 of 6 XP_047301964.1
AKAP19XM_047446009.1 linkc.-518+67568T>C 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+67419T>C intron_variant Intron 1 of 1 4
C2orf88ENST00000495546.1 linkn.201+67419T>C intron_variant Intron 1 of 2 4

Frequencies

GnomAD3 genomes
AF:
0.178
AC:
27029
AN:
152038
Hom.:
2463
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.198
Gnomad AMI
AF:
0.0901
Gnomad AMR
AF:
0.140
Gnomad ASJ
AF:
0.233
Gnomad EAS
AF:
0.106
Gnomad SAS
AF:
0.158
Gnomad FIN
AF:
0.157
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.181
Gnomad OTH
AF:
0.190
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.178
AC:
27050
AN:
152156
Hom.:
2465
Cov.:
33
AF XY:
0.175
AC XY:
13039
AN XY:
74390
show subpopulations
African (AFR)
AF:
0.199
AC:
8242
AN:
41518
American (AMR)
AF:
0.140
AC:
2142
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.233
AC:
809
AN:
3470
East Asian (EAS)
AF:
0.106
AC:
548
AN:
5182
South Asian (SAS)
AF:
0.158
AC:
762
AN:
4828
European-Finnish (FIN)
AF:
0.157
AC:
1662
AN:
10594
Middle Eastern (MID)
AF:
0.262
AC:
77
AN:
294
European-Non Finnish (NFE)
AF:
0.181
AC:
12319
AN:
67950
Other (OTH)
AF:
0.192
AC:
407
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1157
2314
3471
4628
5785
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
292
584
876
1168
1460
<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:
0.183
Hom.:
935
Bravo
AF:
0.178
Asia WGS
AF:
0.166
AC:
579
AN:
3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.6
DANN
Benign
0.75
PhyloP100
0.094

Splicing

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

Publications

Other links and lift over

dbSNP: rs7564968; hg19: chr2-190811972; API