rs6658424

Positions:

• chr1-200080174-T-A

Variant summary

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

The NM_205860.3(NR5A2):​c.1111-31028T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,942 control chromosomes in the GnomAD database, including 6,267 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 0.29 (6267 hom., cov: 32)
• Consequence: NR5A2 NM_205860.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NR5A2	NM_205860.3	c.1111-31028T>A		intron_variant		ENST00000367362.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NR5A2	ENST00000367362.8	c.1111-31028T>A		intron_variant		1	NM_205860.3	A1
NR5A2	ENST00000236914.7	c.973-31028T>A		intron_variant		1		A1
NR5A2	ENST00000544748.5	c.895-31028T>A		intron_variant		2		P4

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43429 AN: 151826 Hom.: 6266 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.286 AC: 43440 AN: 151942 Hom.: 6267 Cov.: 32 AF XY: 0.284 AC XY: 21084 AN XY: 74242

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.298

Alfa AF: 0.292 Hom.: 794

Bravo AF: 0.285

Asia WGS AF: 0.220 AC: 764 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.4
DANN	Benign	0.73

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: rs6658424; hg19: chr1-200049302;