chr1-200116586-T-A

Variant names:

• chr1-200116586-T-A
• rs2821332
• NM_205860.3:c.1231-4222T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_205860.3(NR5A2):​c.1231-4222T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,970 control chromosomes in the GnomAD database, including 13,866 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 0.42 (13866 hom., cov: 32)
• Consequence: NR5A2 NM_205860.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 6 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=-0.89).
• 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.1231-4222T>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.1231-4222T>A		intron_variant	Intron 6 of 7	1	NM_205860.3	ENSP00000356331.3
NR5A2	ENST00000236914.7	c.1093-4222T>A		intron_variant	Intron 5 of 6	1		ENSP00000236914.3
NR5A2	ENST00000544748.5	c.1015-4222T>A		intron_variant	Intron 5 of 6	2		ENSP00000439116.1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63702 AN: 151852 Hom.: 13858 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.419 AC: 63735 AN: 151970 Hom.: 13866 Cov.: 32 AF XY: 0.425 AC XY: 31594 AN XY: 74264

African (AFR) AF: 0.332 AC: 13752 AN: 41430

American (AMR) AF: 0.440 AC: 6714 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1284 AN: 3458

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

South Asian (SAS) AF: 0.519 AC: 2505 AN: 4824

European-Finnish (FIN) AF: 0.501 AC: 5288 AN: 10550

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29188 AN: 67948

Other (OTH) AF: 0.414 AC: 876 AN: 2116

Alfa AF: 0.406 Hom.: 1507

Bravo AF: 0.416

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.61
PhyloP100		-1.3
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: rs2821332; hg19: chr1-200085714;