Variant chr1-200111336-C-CAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_205860.3(NR5A2):c.1230+29_1230+30dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 1,383,324 control chromosomes in the GnomAD database, including 1,856 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 1138 hom., cov: 27)

Exomes 𝑓: 0.079 ( 718 hom. )

Consequence

NR5A2
NM_205860.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.881

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 -10 ACMG points.

BP6

Variant 1-200111336-C-CAA is Benign according to our data. Variant chr1-200111336-C-CAA is described in ClinVar as [Benign]. Clinvar id is 403261.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NR5A2	NM_205860.3 linkuse as main transcript	c.1230+29_1230+30dup		intron_variant		ENST00000367362.8	NP_995582.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
NR5A2	ENST00000367362.8 linkuse as main transcript	c.1230+29_1230+30dup	intron_variant	1	NM_205860.3	ENSP00000356331	A1	O00482-1
NR5A2	ENST00000236914.7 linkuse as main transcript	c.1092+29_1092+30dup	intron_variant	1		ENSP00000236914	A1	O00482-2
NR5A2	ENST00000544748.5 linkuse as main transcript	c.1014+29_1014+30dup	intron_variant	2		ENSP00000439116	P4	O00482-4

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

16297

AN:

126258

Hom.:

1136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.0420

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.00582

Gnomad SAS

AF:

0.0433

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.131

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.123

GnomAD3 exomes

AF:

0.0480

AC:

4906

AN:

102246

Hom.:

397

AF XY:

0.0441

AC XY:

2426

AN XY:

54958

show subpopulations

Gnomad AFR exome

AF:

0.0838

Gnomad AMR exome

AF:

0.0411

Gnomad ASJ exome

AF:

0.0673

Gnomad EAS exome

AF:

0.0116

Gnomad SAS exome

AF:

0.0194

Gnomad FIN exome

AF:

0.0400

Gnomad NFE exome

AF:

0.0555

Gnomad OTH exome

AF:

0.0512

GnomAD4 exome

AF:

0.0787

AC:

98940

AN:

1257050

Hom.:

718

Cov.:

AF XY:

0.0763

AC XY:

47498

AN XY:

622444

show subpopulations

Gnomad4 AFR exome

AF:

0.107

Gnomad4 AMR exome

AF:

0.0434

Gnomad4 ASJ exome

AF:

0.0975

Gnomad4 EAS exome

AF:

0.0124

Gnomad4 SAS exome

AF:

0.0274

Gnomad4 FIN exome

AF:

0.0583

Gnomad4 NFE exome

AF:

0.0853

Gnomad4 OTH exome

AF:

0.0759

GnomAD4 genome

AF:

0.129

AC:

16299

AN:

126274

Hom.:

1138

Cov.:

AF XY:

0.124

AC XY:

7494

AN XY:

60674

show subpopulations

Gnomad4 AFR

AF:

0.152

Gnomad4 AMR

AF:

0.0997

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.00583

Gnomad4 SAS

AF:

0.0436

Gnomad4 FIN

AF:

0.100

Gnomad4 NFE

AF:

0.139

Gnomad4 OTH

AF:

0.123

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency, outside ROI -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over