GeneBe

rs76894039

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_205860.3(NR5A2):​c.1230+24_1230+30delAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000078 in 1,281,362 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 27)
Exomes 𝑓: 7.8e-7 ( 0 hom. )

Consequence

NR5A2
NM_205860.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.987

Publications

0 publications found
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 was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_205860.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NR5A2
NM_205860.3
MANE Select
c.1230+24_1230+30delAAAAAAA
intron
N/ANP_995582.1
NR5A2
NM_003822.5
c.1092+24_1092+30delAAAAAAA
intron
N/ANP_003813.1
NR5A2
NM_001276464.2
c.1014+24_1014+30delAAAAAAA
intron
N/ANP_001263393.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
NR5A2
ENST00000367362.8
TSL:1 MANE Select
c.1230+16_1230+22delAAAAAAA
intron
N/AENSP00000356331.3
NR5A2
ENST00000236914.7
TSL:1
c.1092+16_1092+22delAAAAAAA
intron
N/AENSP00000236914.3
NR5A2
ENST00000892175.1
c.1155+16_1155+22delAAAAAAA
intron
N/AENSP00000562234.1

Frequencies

GnomAD3 genomes
Cov.:
27
GnomAD4 exome
AF:
7.80e-7
AC:
1
AN:
1281362
Hom.:
0
AF XY:
0.00000158
AC XY:
1
AN XY:
634170
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.0000378
AC:
1
AN:
26438
American (AMR)
AF:
0.00
AC:
0
AN:
25874
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20124
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35216
South Asian (SAS)
AF:
0.00
AC:
0
AN:
67742
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
36976
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4628
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1011484
Other (OTH)
AF:
0.00
AC:
0
AN:
52880
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.99

Splicing

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

Publications

Other links and lift over

dbSNP: rs76894039; hg19: chr1-200080464; API