rs200681711

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001371702.1(CYP20A1):​c.-242A>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,460,146 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 27)
Exomes 𝑓: 0.0000089 ( 0 hom. )

Consequence

CYP20A1
NM_001371702.1 5_prime_UTR_premature_start_codon_gain

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.444
Variant links:
Genes affected
CYP20A1 (HGNC:20576): (cytochrome P450 family 20 subfamily A member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases that catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein lacks one amino acid of the conserved heme binding site. It also lacks the conserved I-helix motif AGX(D,E)T, suggesting that its substrate may carry its own oxygen. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08145812).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CYP20A1NM_177538.3 linkc.364A>C p.Met122Leu missense_variant Exon 4 of 13 ENST00000356079.9 NP_803882.1 Q6UW02-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CYP20A1ENST00000356079.9 linkc.364A>C p.Met122Leu missense_variant Exon 4 of 13 1 NM_177538.3 ENSP00000348380.4 Q6UW02-1

Frequencies

GnomAD3 genomes
Cov.:
27
GnomAD3 exomes
AF:
0.0000160
AC:
4
AN:
250352
Hom.:
0
AF XY:
0.0000148
AC XY:
2
AN XY:
135370
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000353
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000890
AC:
13
AN:
1460146
Hom.:
0
Cov.:
32
AF XY:
0.0000110
AC XY:
8
AN XY:
726430
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000108
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
27
Alfa
AF:
0.00000551
Hom.:
0
Bravo
AF:
0.00000378
ExAC
AF:
0.0000165
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.071
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
8.0
DANN
Benign
0.44
DEOGEN2
Benign
0.031
T;T;T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.73
D
LIST_S2
Benign
0.68
T;T;T
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.081
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.20
N;.;.
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.47
N;N;N
REVEL
Benign
0.17
Sift
Benign
0.46
T;T;T
Sift4G
Benign
0.55
T;T;T
Polyphen
0.0
B;B;.
Vest4
0.13
MutPred
0.55
Gain of catalytic residue at M122 (P = 0.0516);Gain of catalytic residue at M122 (P = 0.0516);Gain of catalytic residue at M122 (P = 0.0516);
MVP
0.62
MPC
0.10
ClinPred
0.013
T
GERP RS
-3.2
Varity_R
0.036
gMVP
0.30

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200681711; hg19: chr2-204116764; API