rs41300849
Positions:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1
The NM_205860.3(NR5A2):c.322-11C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 1,562,174 control chromosomes in the GnomAD database, including 6,308 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 0.081 ( 533 hom., cov: 33)
Exomes 𝑓: 0.087 ( 5775 hom. )
Consequence
NR5A2
NM_205860.3 splice_polypyrimidine_tract, intron
NM_205860.3 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.3595
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.88
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.17).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0981 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR5A2 | NM_205860.3 | c.322-11C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000367362.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR5A2 | ENST00000367362.8 | c.322-11C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_205860.3 | A1 | |||
NR5A2 | ENST00000236914.7 | c.184-11C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
NR5A2 | ENST00000367357.3 | c.84-11C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
NR5A2 | ENST00000544748.5 | c.106-11C>T | splice_polypyrimidine_tract_variant, intron_variant | 2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0810 AC: 12321AN: 152064Hom.: 532 Cov.: 33
GnomAD3 genomes
AF:
AC:
12321
AN:
152064
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0730 AC: 15401AN: 210846Hom.: 649 AF XY: 0.0732 AC XY: 8415AN XY: 114958
GnomAD3 exomes
AF:
AC:
15401
AN:
210846
Hom.:
AF XY:
AC XY:
8415
AN XY:
114958
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0869 AC: 122505AN: 1409992Hom.: 5775 Cov.: 29 AF XY: 0.0863 AC XY: 60489AN XY: 700852
GnomAD4 exome
AF:
AC:
122505
AN:
1409992
Hom.:
Cov.:
29
AF XY:
AC XY:
60489
AN XY:
700852
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0810 AC: 12332AN: 152182Hom.: 533 Cov.: 33 AF XY: 0.0776 AC XY: 5775AN XY: 74420
GnomAD4 genome
AF:
AC:
12332
AN:
152182
Hom.:
Cov.:
33
AF XY:
AC XY:
5775
AN XY:
74420
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
159
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at