1-200041696-C-T

Variant names:

• chr1-200041696-C-T
• rs3790843
• NM_205860.3:c.202+1901C>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.202+1901C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,008 control chromosomes in the GnomAD database, including 8,275 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 0.30 (8275 hom., cov: 32)
• Consequence: NR5A2 NM_205860.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.773
• Publications: 18 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_205860.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR5A2	NM_205860.3	MANE Select	c.202+1901C>T		intron	N/A	NP_995582.1	O00482-1
	NR5A2	NM_003822.5		c.65-2078C>T		intron	N/A	NP_003813.1	F1D8R9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR5A2	ENST00000367362.8	TSL:1 MANE Select	c.202+1901C>T		intron	N/A	ENSP00000356331.3	O00482-1
	NR5A2	ENST00000236914.7	TSL:1	c.65-2078C>T		intron	N/A	ENSP00000236914.3	O00482-2
	NR5A2	ENST00000474307.1	TSL:1	n.*419-2078C>T		intron	N/A	ENSP00000436776.1	E9PQH2

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45308 AN: 151890 Hom.: 8256 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.298 AC: 45332 AN: 152008 Hom.: 8275 Cov.: 32 AF XY: 0.312 AC XY: 23221 AN XY: 74318

African (AFR) AF: 0.140 AC: 5794 AN: 41490

American (AMR) AF: 0.422 AC: 6450 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 883 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3622 AN: 5136

South Asian (SAS) AF: 0.516 AC: 2486 AN: 4820

European-Finnish (FIN) AF: 0.450 AC: 4745 AN: 10556

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20362 AN: 67930

Other (OTH) AF: 0.287 AC: 606 AN: 2114

Alfa AF: 0.308 Hom.: 8980

Bravo AF: 0.289

Asia WGS AF: 0.564 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	10
DANN	Benign	0.50
PhyloP100		0.77
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3790843; hg19: chr1-200010824;