rs3828107

Positions:

• chr1-200151899-A-G
• chr1-200151899-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_205860.3(NR5A2):​c.1379-22064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0622 in 152,310 control chromosomes in the GnomAD database, including 468 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 0.062 (468 hom., cov: 33)
• Consequence: NR5A2 NM_205860.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NR5A2	NM_205860.3	c.1379-22064A>G		intron_variant		ENST00000367362.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NR5A2	ENST00000367362.8	c.1379-22064A>G		intron_variant		1	NM_205860.3	A1
NR5A2	ENST00000236914.7	c.1241-22064A>G		intron_variant		1		A1
NR5A2	ENST00000544748.5	c.1163-22064A>G		intron_variant		2		P4

Frequencies

GnomAD3 genomes AF: 0.0622 AC: 9465 AN: 152192 Hom.: 469 Cov.: 33

Gnomad AFR AF: 0.0639

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0394

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.0593

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0622 AC: 9468 AN: 152310 Hom.: 468 Cov.: 33 AF XY: 0.0636 AC XY: 4738 AN XY: 74482

Gnomad4 AFR AF: 0.0639

Gnomad4 AMR AF: 0.0769

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.0394

Gnomad4 NFE AF: 0.0440

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0478 Hom.: 289

Bravo AF: 0.0678

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.59

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

Other links and lift over

dbSNP: rs3828107; hg19: chr1-200121027;