rs12078096
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_205860.3(NR5A2):c.1379-13022A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 151,984 control chromosomes in the GnomAD database, including 416 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 0.048 ( 416 hom., cov: 31)
Consequence
NR5A2
NM_205860.3 intron
NM_205860.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.45
Genes affected
NR5A2 (HGNC:7984): (nuclear receptor subfamily 5 group A member 2) The protein encoded by this gene is a DNA-binding zinc finger transcription factor and is a member of the fushi tarazu factor-1 subfamily of orphan nuclear receptors. The encoded protein is involved in the expression of genes for hepatitis B virus and cholesterol biosynthesis, and may be an important regulator of embryonic development. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR5A2 | NM_205860.3 | c.1379-13022A>C | intron_variant | ENST00000367362.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR5A2 | ENST00000367362.8 | c.1379-13022A>C | intron_variant | 1 | NM_205860.3 | A1 | |||
NR5A2 | ENST00000236914.7 | c.1241-13022A>C | intron_variant | 1 | A1 | ||||
NR5A2 | ENST00000544748.5 | c.1163-13022A>C | intron_variant | 2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0478 AC: 7257AN: 151866Hom.: 415 Cov.: 31
GnomAD3 genomes
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0478 AC: 7268AN: 151984Hom.: 416 Cov.: 31 AF XY: 0.0494 AC XY: 3672AN XY: 74300
GnomAD4 genome
?
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7268
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151984
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31
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3672
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74300
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154
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at