rs4646
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000103.4(CYP19A1):c.*161T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 752,108 control chromosomes in the GnomAD database, including 187,141 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000103.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYP19A1 | NM_000103.4 | c.*161T>G | 3_prime_UTR_variant | Exon 10 of 10 | ENST00000396402.6 | NP_000094.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYP19A1 | ENST00000396402 | c.*161T>G | 3_prime_UTR_variant | Exon 10 of 10 | 1 | NM_000103.4 | ENSP00000379683.1 | |||
CYP19A1 | ENST00000559878 | c.*161T>G | 3_prime_UTR_variant | Exon 9 of 9 | 1 | ENSP00000453149.1 | ||||
CYP19A1 | ENST00000396404 | c.*161T>G | 3_prime_UTR_variant | Exon 11 of 11 | 2 | ENSP00000379685.4 | ||||
MIR4713HG | ENST00000559909.1 | n.195-67336A>C | intron_variant | Intron 1 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.702 AC: 106604AN: 151928Hom.: 37705 Cov.: 32
GnomAD3 exomes AF: 0.672 AC: 147573AN: 219628Hom.: 50443 AF XY: 0.679 AC XY: 81398AN XY: 119940
GnomAD4 exome AF: 0.701 AC: 420906AN: 600062Hom.: 149410 Cov.: 4 AF XY: 0.702 AC XY: 230169AN XY: 327918
GnomAD4 genome AF: 0.702 AC: 106677AN: 152046Hom.: 37731 Cov.: 32 AF XY: 0.698 AC XY: 51840AN XY: 74298
ClinVar
Submissions by phenotype
Aromatase deficiency Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at