rs10494808
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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.1231-64C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000484 in 1,447,638 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 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000046 ( 0 hom. )
Consequence
NR5A2
NM_205860.3 intron
NM_205860.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.154
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=-0.94).
BS2
?
High AC in GnomAdExome4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR5A2 | NM_205860.3 | c.1231-64C>A | intron_variant | ENST00000367362.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR5A2 | ENST00000367362.8 | c.1231-64C>A | intron_variant | 1 | NM_205860.3 | A1 | |||
NR5A2 | ENST00000236914.7 | c.1093-64C>A | intron_variant | 1 | A1 | ||||
NR5A2 | ENST00000544748.5 | c.1015-64C>A | intron_variant | 2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151970Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000463 AC: 6AN: 1295668Hom.: 0 AF XY: 0.00000630 AC XY: 4AN XY: 635258
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GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151970Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74214
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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