rs3828110
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_205860.3(NR5A2):c.1230+14C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000417 in 1,197,646 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: 𝑓 0.00011 ( 0 hom., cov: 14)
Exomes 𝑓: 0.000042 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
NR5A2
NM_205860.3 intron
NM_205860.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0380
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BS2
?
High AC in GnomAdExome4 at 50 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR5A2 | NM_205860.3 | c.1230+14C>A | intron_variant | ENST00000367362.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR5A2 | ENST00000367362.8 | c.1230+14C>A | intron_variant | 1 | NM_205860.3 | A1 | |||
NR5A2 | ENST00000236914.7 | c.1092+14C>A | intron_variant | 1 | A1 | ||||
NR5A2 | ENST00000544748.5 | c.1014+14C>A | intron_variant | 2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 9AN: 82384Hom.: 0 Cov.: 14 FAILED QC
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GnomAD3 exomes AF: 0.0000316 AC: 4AN: 126484Hom.: 0 AF XY: 0.0000433 AC XY: 3AN XY: 69340
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GnomAD4 exome AF: 0.0000417 AC: 50AN: 1197646Hom.: 0 Cov.: 29 AF XY: 0.0000370 AC XY: 22AN XY: 594262
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000109 AC: 9AN: 82384Hom.: 0 Cov.: 14 AF XY: 0.000126 AC XY: 5AN XY: 39552
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
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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