rs3828112

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_205860.3(NR5A2):​c.1110+24085T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,970 control chromosomes in the GnomAD database, including 6,277 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 0.29 ( 6277 hom., cov: 31)

Consequence

NR5A2
NM_205860.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NR5A2NM_205860.3 linkuse as main transcriptc.1110+24085T>C intron_variant ENST00000367362.8 NP_995582.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NR5A2ENST00000367362.8 linkuse as main transcriptc.1110+24085T>C intron_variant 1 NM_205860.3 ENSP00000356331 A1O00482-1
NR5A2ENST00000236914.7 linkuse as main transcriptc.972+24085T>C intron_variant 1 ENSP00000236914 A1O00482-2
NR5A2ENST00000544748.5 linkuse as main transcriptc.894+24085T>C intron_variant 2 ENSP00000439116 P4O00482-4

Frequencies

GnomAD3 genomes
AF:
0.286
AC:
43486
AN:
151852
Hom.:
6276
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.288
Gnomad AMI
AF:
0.346
Gnomad AMR
AF:
0.269
Gnomad ASJ
AF:
0.370
Gnomad EAS
AF:
0.195
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.298
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.293
Gnomad OTH
AF:
0.298
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.286
AC:
43497
AN:
151970
Hom.:
6277
Cov.:
31
AF XY:
0.284
AC XY:
21121
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.287
Gnomad4 AMR
AF:
0.269
Gnomad4 ASJ
AF:
0.370
Gnomad4 EAS
AF:
0.195
Gnomad4 SAS
AF:
0.231
Gnomad4 FIN
AF:
0.298
Gnomad4 NFE
AF:
0.293
Gnomad4 OTH
AF:
0.297
Alfa
AF:
0.298
Hom.:
13903
Bravo
AF:
0.285
Asia WGS
AF:
0.224
AC:
777
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
14
DANN
Benign
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3828112; hg19: chr1-200042031; API