1-200067011-C-T

Variant summary

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

The NM_205860.3(NR5A2):​c.1110+18193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,168 control chromosomes in the GnomAD database, including 4,607 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 0.21 ( 4607 hom., cov: 33)

Consequence

NR5A2
NM_205860.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.680
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NR5A2NM_205860.3 linkuse as main transcriptc.1110+18193C>T intron_variant ENST00000367362.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NR5A2ENST00000367362.8 linkuse as main transcriptc.1110+18193C>T intron_variant 1 NM_205860.3 A1O00482-1
NR5A2ENST00000236914.7 linkuse as main transcriptc.972+18193C>T intron_variant 1 A1O00482-2
NR5A2ENST00000544748.5 linkuse as main transcriptc.894+18193C>T intron_variant 2 P4O00482-4

Frequencies

GnomAD3 genomes
AF:
0.214
AC:
32606
AN:
152050
Hom.:
4592
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.407
Gnomad AMI
AF:
0.203
Gnomad AMR
AF:
0.168
Gnomad ASJ
AF:
0.215
Gnomad EAS
AF:
0.189
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.134
Gnomad MID
AF:
0.232
Gnomad NFE
AF:
0.129
Gnomad OTH
AF:
0.196
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.215
AC:
32665
AN:
152168
Hom.:
4607
Cov.:
33
AF XY:
0.212
AC XY:
15740
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.407
Gnomad4 AMR
AF:
0.168
Gnomad4 ASJ
AF:
0.215
Gnomad4 EAS
AF:
0.188
Gnomad4 SAS
AF:
0.128
Gnomad4 FIN
AF:
0.134
Gnomad4 NFE
AF:
0.129
Gnomad4 OTH
AF:
0.195
Alfa
AF:
0.146
Hom.:
2431
Bravo
AF:
0.225
Asia WGS
AF:
0.173
AC:
602
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
3.2
DANN
Benign
0.82

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: rs12069549; hg19: chr1-200036139; COSMIC: COSV52647084; API