chr10-94988878-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000771.4(CYP2C9):c.1323C>T(p.Ala441Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00592 in 1,613,836 control chromosomes in the GnomAD database, including 414 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.030 ( 242 hom., cov: 32)
Exomes 𝑓: 0.0034 ( 172 hom. )
Consequence
CYP2C9
NM_000771.4 synonymous
NM_000771.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0580
Publications
15 publications found
Genes affected
CYP2C9 (HGNC:2623): (cytochrome P450 family 2 subfamily C member 9) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and its expression is induced by rifampin. The enzyme is known to metabolize many xenobiotics, including phenytoin, tolbutamide, ibuprofen and S-warfarin. Studies identifying individuals who are poor metabolizers of phenytoin and tolbutamide suggest that this gene is polymorphic. The gene is located within a cluster of cytochrome P450 genes on chromosome 10q24. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
Variant 10-94988878-C-T is Benign according to our data. Variant chr10-94988878-C-T is described in ClinVar as Benign. ClinVar VariationId is 776530.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.058 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP2C9 | ENST00000260682.8 | c.1323C>T | p.Ala441Ala | synonymous_variant | Exon 9 of 9 | 1 | NM_000771.4 | ENSP00000260682.6 | ||
CYP2C9 | ENST00000643112.1 | n.*332C>T | non_coding_transcript_exon_variant | Exon 8 of 8 | ENSP00000496202.1 | |||||
CYP2C9 | ENST00000643112.1 | n.*332C>T | 3_prime_UTR_variant | Exon 8 of 8 | ENSP00000496202.1 |
Frequencies
GnomAD3 genomes AF: 0.0305 AC: 4641AN: 152104Hom.: 242 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
4641
AN:
152104
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00847 AC: 2130AN: 251376 AF XY: 0.00654 show subpopulations
GnomAD2 exomes
AF:
AC:
2130
AN:
251376
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00337 AC: 4921AN: 1461614Hom.: 172 Cov.: 32 AF XY: 0.00294 AC XY: 2136AN XY: 727124 show subpopulations
GnomAD4 exome
AF:
AC:
4921
AN:
1461614
Hom.:
Cov.:
32
AF XY:
AC XY:
2136
AN XY:
727124
show subpopulations
African (AFR)
AF:
AC:
3361
AN:
33448
American (AMR)
AF:
AC:
371
AN:
44700
Ashkenazi Jewish (ASJ)
AF:
AC:
32
AN:
26128
East Asian (EAS)
AF:
AC:
1
AN:
39698
South Asian (SAS)
AF:
AC:
14
AN:
86252
European-Finnish (FIN)
AF:
AC:
1
AN:
53418
Middle Eastern (MID)
AF:
AC:
67
AN:
5728
European-Non Finnish (NFE)
AF:
AC:
611
AN:
1111858
Other (OTH)
AF:
AC:
463
AN:
60384
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.468
Heterozygous variant carriers
0
288
577
865
1154
1442
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
120
240
360
480
600
<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: 0.0305 AC: 4638AN: 152222Hom.: 242 Cov.: 32 AF XY: 0.0291 AC XY: 2163AN XY: 74436 show subpopulations
GnomAD4 genome
AF:
AC:
4638
AN:
152222
Hom.:
Cov.:
32
AF XY:
AC XY:
2163
AN XY:
74436
show subpopulations
African (AFR)
AF:
AC:
4291
AN:
41508
American (AMR)
AF:
AC:
246
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
3
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5174
South Asian (SAS)
AF:
AC:
1
AN:
4830
European-Finnish (FIN)
AF:
AC:
1
AN:
10610
Middle Eastern (MID)
AF:
AC:
7
AN:
294
European-Non Finnish (NFE)
AF:
AC:
43
AN:
68026
Other (OTH)
AF:
AC:
46
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
203
406
610
813
1016
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
52
104
156
208
260
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
17
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Jun 26, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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