rs2249172

Variant names:

• chr1-200113827-G-A
• rs2249172
• NM_205860.3:c.1230+2506G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-200113827-G-A
• chr1-200113827-G-C
• chr1-200113827-G-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.1230+2506G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,914 control chromosomes in the GnomAD database, including 14,707 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 0.43 (14707 hom., cov: 32)
• Consequence: NR5A2 NM_205860.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR5A2	NM_205860.3	c.1230+2506G>A		intron_variant	Intron 6 of 7	ENST00000367362.8	NP_995582.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR5A2	ENST00000367362.8	c.1230+2506G>A		intron_variant	Intron 6 of 7	1	NM_205860.3	ENSP00000356331.3
NR5A2	ENST00000236914.7	c.1092+2506G>A		intron_variant	Intron 5 of 6	1		ENSP00000236914.3
NR5A2	ENST00000544748.5	c.1014+2506G>A		intron_variant	Intron 5 of 6	2		ENSP00000439116.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65983 AN: 151796 Hom.: 14700 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.435 AC: 66016 AN: 151914 Hom.: 14707 Cov.: 32 AF XY: 0.440 AC XY: 32664 AN XY: 74226

African (AFR) AF: 0.366 AC: 15173 AN: 41400

American (AMR) AF: 0.449 AC: 6849 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3468

East Asian (EAS) AF: 0.678 AC: 3512 AN: 5180

South Asian (SAS) AF: 0.522 AC: 2510 AN: 4810

European-Finnish (FIN) AF: 0.504 AC: 5309 AN: 10530

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29869 AN: 67956

Other (OTH) AF: 0.429 AC: 902 AN: 2102

Alfa AF: 0.430 Hom.: 2179

Bravo AF: 0.432

Asia WGS AF: 0.539 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		0.22
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: rs2249172; hg19: chr1-200082955;