Variant 1-200045432-C-T details in Genebe, Genetics Data Aggregator

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

Scores

Splicing: ADA: 0.3595

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.88

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]

NR5A2 links:

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 linkuse as main transcript	c.322-11C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000367362.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
NR5A2	ENST00000367362.8 linkuse as main transcript	c.322-11C>T	splice_polypyrimidine_tract_variant, intron_variant	1	NM_205860.3	A1	O00482-1
NR5A2	ENST00000236914.7 linkuse as main transcript	c.184-11C>T	splice_polypyrimidine_tract_variant, intron_variant	1		A1	O00482-2
NR5A2	ENST00000367357.3 linkuse as main transcript	c.84-11C>T	splice_polypyrimidine_tract_variant, intron_variant	1
NR5A2	ENST00000544748.5 linkuse as main transcript	c.106-11C>T	splice_polypyrimidine_tract_variant, intron_variant	2		P4	O00482-4

Frequencies

GnomAD3 genomes

AF:

0.0810

AC:

12321

AN:

152064

Hom.:

532

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0729

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0687

Gnomad ASJ

AF:

0.0676

Gnomad EAS

AF:

0.0181

Gnomad SAS

AF:

0.0573

Gnomad FIN

AF:

0.0507

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.100

Gnomad OTH

AF:

0.0825

GnomAD3 exomes

AF:

0.0730

AC:

15401

AN:

210846

Hom.:

649

AF XY:

0.0732

AC XY:

8415

AN XY:

114958

show subpopulations

Gnomad AFR exome

AF:

0.0728

Gnomad AMR exome

AF:

0.0412

Gnomad ASJ exome

AF:

0.0675

Gnomad EAS exome

AF:

0.0177

Gnomad SAS exome

AF:

0.0576

Gnomad FIN exome

AF:

0.0544

Gnomad NFE exome

AF:

0.0961

Gnomad OTH exome

AF:

0.0783

GnomAD4 exome

AF:

0.0869

AC:

122505

AN:

1409992

Hom.:

5775

Cov.:

AF XY:

0.0863

AC XY:

60489

AN XY:

700852

show subpopulations

Gnomad4 AFR exome

AF:

0.0663

Gnomad4 AMR exome

AF:

0.0460

Gnomad4 ASJ exome

AF:

0.0646

Gnomad4 EAS exome

AF:

0.0216

Gnomad4 SAS exome

AF:

0.0577

Gnomad4 FIN exome

AF:

0.0582

Gnomad4 NFE exome

AF:

0.0953

Gnomad4 OTH exome

AF:

0.0844

GnomAD4 genome

AF:

0.0810

AC:

12332

AN:

152182

Hom.:

533

Cov.:

AF XY:

0.0776

AC XY:

5775

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.0729

Gnomad4 AMR

AF:

0.0686

Gnomad4 ASJ

AF:

0.0676

Gnomad4 EAS

AF:

0.0179

Gnomad4 SAS

AF:

0.0576

Gnomad4 FIN

AF:

0.0507

Gnomad4 NFE

AF:

0.100

Gnomad4 OTH

AF:

0.0826

Alfa

AF:

0.0858

Hom.:

105

Bravo

AF:

0.0798

Asia WGS

AF:

0.0460

AC:

159

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.17

CADD

Benign

DANN

Benign

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.36

dbscSNV1_RF

Benign

0.54

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over