chr1-200116586-T-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_205860.3(NR5A2):​c.1231-4222T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,970 control chromosomes in the GnomAD database, including 13,866 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 0.42 ( 13866 hom., cov: 32)

Consequence

NR5A2
NM_205860.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.25
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NR5A2NM_205860.3 linkc.1231-4222T>A intron_variant Intron 6 of 7 ENST00000367362.8 NP_995582.1 O00482-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NR5A2ENST00000367362.8 linkc.1231-4222T>A intron_variant Intron 6 of 7 1 NM_205860.3 ENSP00000356331.3 O00482-1
NR5A2ENST00000236914.7 linkc.1093-4222T>A intron_variant Intron 5 of 6 1 ENSP00000236914.3 O00482-2
NR5A2ENST00000544748.5 linkc.1015-4222T>A intron_variant Intron 5 of 6 2 ENSP00000439116.1 O00482-4

Frequencies

GnomAD3 genomes
AF:
0.420
AC:
63702
AN:
151852
Hom.:
13858
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.332
Gnomad AMI
AF:
0.530
Gnomad AMR
AF:
0.441
Gnomad ASJ
AF:
0.371
Gnomad EAS
AF:
0.678
Gnomad SAS
AF:
0.519
Gnomad FIN
AF:
0.501
Gnomad MID
AF:
0.462
Gnomad NFE
AF:
0.430
Gnomad OTH
AF:
0.407
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.419
AC:
63735
AN:
151970
Hom.:
13866
Cov.:
32
AF XY:
0.425
AC XY:
31594
AN XY:
74264
show subpopulations
African (AFR)
AF:
0.332
AC:
13752
AN:
41430
American (AMR)
AF:
0.440
AC:
6714
AN:
15260
Ashkenazi Jewish (ASJ)
AF:
0.371
AC:
1284
AN:
3458
East Asian (EAS)
AF:
0.678
AC:
3512
AN:
5180
South Asian (SAS)
AF:
0.519
AC:
2505
AN:
4824
European-Finnish (FIN)
AF:
0.501
AC:
5288
AN:
10550
Middle Eastern (MID)
AF:
0.456
AC:
134
AN:
294
European-Non Finnish (NFE)
AF:
0.430
AC:
29188
AN:
67948
Other (OTH)
AF:
0.414
AC:
876
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1852
3704
5557
7409
9261
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
618
1236
1854
2472
3090
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.406
Hom.:
1507
Bravo
AF:
0.416
Asia WGS
AF:
0.532
AC:
1849
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.28
DANN
Benign
0.61
PhyloP100
-1.3
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2821332; hg19: chr1-200085714; API