rs2821368
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_205860.3(NR5A2):āc.750C>Gā(p.Pro250=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 1,613,982 control chromosomes in the GnomAD database, including 32,724 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: š 0.26 ( 6860 hom., cov: 32)
Exomes š: 0.18 ( 25864 hom. )
Consequence
NR5A2
NM_205860.3 synonymous
NM_205860.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0950
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP7
?
Synonymous conserved (PhyloP=-0.095 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR5A2 | NM_205860.3 | c.750C>G | p.Pro250= | synonymous_variant | 5/8 | ENST00000367362.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR5A2 | ENST00000367362.8 | c.750C>G | p.Pro250= | synonymous_variant | 5/8 | 1 | NM_205860.3 | A1 | |
NR5A2 | ENST00000236914.7 | c.612C>G | p.Pro204= | synonymous_variant | 4/7 | 1 | A1 | ||
NR5A2 | ENST00000367357.3 | c.513C>G | p.Pro171= | synonymous_variant | 3/4 | 1 | |||
NR5A2 | ENST00000544748.5 | c.534C>G | p.Pro178= | synonymous_variant | 4/7 | 2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.261 AC: 39604AN: 152000Hom.: 6845 Cov.: 32
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GnomAD3 exomes AF: 0.183 AC: 46071AN: 251412Hom.: 5460 AF XY: 0.178 AC XY: 24240AN XY: 135880
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GnomAD4 exome AF: 0.176 AC: 257721AN: 1461864Hom.: 25864 Cov.: 36 AF XY: 0.175 AC XY: 127097AN XY: 727232
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GnomAD4 genome ? AF: 0.261 AC: 39657AN: 152118Hom.: 6860 Cov.: 32 AF XY: 0.258 AC XY: 19167AN XY: 74356
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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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at