15-51242798-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_000103.4(CYP19A1):c.115T>A(p.Trp39Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar.
Frequency
Genomes: not found (cov: 32)
Consequence
CYP19A1
NM_000103.4 missense
NM_000103.4 missense
Scores
4
8
6
Clinical Significance
Conservation
PhyloP100: 4.40
Genes affected
CYP19A1 (HGNC:2594): (cytochrome P450 family 19 subfamily A member 1) 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 catalyzes the last steps of estrogen biosynthesis. Mutations in this gene can result in either increased or decreased aromatase activity; the associated phenotypes suggest that estrogen functions both as a sex steroid hormone and in growth or differentiation. Alternative promoter use and alternative splicing results in multiple transcript variants that have different tissue specificities. [provided by RefSeq, Dec 2016]
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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;
BP6
?
Variant 15-51242798-A-T is Benign according to our data. Variant chr15-51242798-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1606711.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP19A1 | NM_000103.4 | c.115T>A | p.Trp39Arg | missense_variant | 2/10 | ENST00000396402.6 | |
MIR4713HG | NR_146310.1 | n.195-35185A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP19A1 | ENST00000396402.6 | c.115T>A | p.Trp39Arg | missense_variant | 2/10 | 1 | NM_000103.4 | P1 | |
MIR4713HG | ENST00000559909.1 | n.195-35185A>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 25
GnomAD4 exome
Cov.:
25
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Benign
Dann
Uncertain
DEOGEN2
Uncertain
D;D;D;.;T;.;.;.;T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;M;M;.;.;.;M;M;.;.;.
MutationTaster
Benign
D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D
REVEL
Uncertain
Sift
Benign
D;D;D;T;D;D;D;D;D;D;D
Sift4G
Uncertain
T;T;T;T;.;T;T;T;T;T;.
Polyphen
B;B;B;.;.;.;.;.;.;.;.
Vest4
MutPred
Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);Loss of catalytic residue at L37 (P = 0.0025);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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
No publications associated with this variant yet.