GeneBe

10-100120943-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 0.388 in 146,876 control chromosomes in the GnomAD database, including 11,311 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 0.39 ( 11310 hom., cov: 25)
Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

CYP2C23P
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.20

Publications

12 publications found
Variant links:
Genes affected
CYP2C23P (HGNC:39970): (cytochrome P450 family 2 subfamily C member 23, pseudogene)

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=-0.96).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CYP2C23P n.100120943C>T intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CYP2C23PENST00000636357.1 linkn.613+5G>A splice_region_variant, intron_variant Intron 4 of 6 6

Frequencies

GnomAD3 genomes
AF:
0.388
AC:
56928
AN:
146790
Hom.:
11298
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.415
Gnomad AMI
AF:
0.552
Gnomad AMR
AF:
0.386
Gnomad ASJ
AF:
0.346
Gnomad EAS
AF:
0.138
Gnomad SAS
AF:
0.231
Gnomad FIN
AF:
0.311
Gnomad MID
AF:
0.448
Gnomad NFE
AF:
0.411
Gnomad OTH
AF:
0.407
GnomAD4 exome
AF:
1.00
AC:
2
AN:
2
Hom.:
1
Cov.:
0
AC XY:
0
AN XY:
0
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
1.00
AC:
2
AN:
2
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome
AF:
0.388
AC:
56987
AN:
146874
Hom.:
11310
Cov.:
25
AF XY:
0.381
AC XY:
27052
AN XY:
71028
show subpopulations
African (AFR)
AF:
0.416
AC:
16544
AN:
39814
American (AMR)
AF:
0.386
AC:
5571
AN:
14434
Ashkenazi Jewish (ASJ)
AF:
0.346
AC:
1197
AN:
3456
East Asian (EAS)
AF:
0.138
AC:
696
AN:
5060
South Asian (SAS)
AF:
0.231
AC:
1081
AN:
4670
European-Finnish (FIN)
AF:
0.311
AC:
2789
AN:
8974
Middle Eastern (MID)
AF:
0.444
AC:
127
AN:
286
European-Non Finnish (NFE)
AF:
0.411
AC:
27657
AN:
67254
Other (OTH)
AF:
0.409
AC:
829
AN:
2028
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1618
3235
4853
6470
8088
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
538
1076
1614
2152
2690
<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:
0.398
Hom.:
34616
Bravo
AF:
0.398
Asia WGS
AF:
0.203
AC:
708
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.0
DANN
Benign
0.21
PhyloP100
-2.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs11594333; hg19: chr10-101880700; API