rs3828107

Variant names:

• chr1-200151899-A-G
• rs3828107
• NM_205860.3:c.1379-22064A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NR5A2	NM_205860.3	c.1379-22064A>G		intron_variant	Intron 7 of 7	ENST00000367362.8	NP_995582.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR5A2	ENST00000367362.8	c.1379-22064A>G		intron_variant	Intron 7 of 7	1	NM_205860.3	ENSP00000356331.3
NR5A2	ENST00000236914.7	c.1241-22064A>G		intron_variant	Intron 6 of 6	1		ENSP00000236914.3
NR5A2	ENST00000544748.5	c.1163-22064A>G		intron_variant	Intron 6 of 6	2		ENSP00000439116.1

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

African (AFR) AF: 0.0639 AC: 2655 AN: 41560

American (AMR) AF: 0.0769 AC: 1177 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3470

East Asian (EAS) AF: 0.285 AC: 1474 AN: 5178

South Asian (SAS) AF: 0.0972 AC: 469 AN: 4824

European-Finnish (FIN) AF: 0.0394 AC: 418 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0440 AC: 2992 AN: 68034

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0487 Hom.: 377

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
PhyloP100		0.85
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3828107; hg19: chr1-200121027;