NM_205860.3:c.1110+24085T>C

Variant names:

• chr1-200072903-T-C
• rs3828112
• NM_205860.3:c.1110+24085T>C

Variant summary

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

The NM_205860.3(NR5A2):​c.1110+24085T>C 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 151,970 control chromosomes in the GnomAD database, including 6,277 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 (6277 hom., cov: 31)
• Consequence: NR5A2 NM_205860.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 3 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=-0.49).
• 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 rank	MANE	Protein	UniProt
NR5A2	NM_205860.3	c.1110+24085T>C		intron_variant	Intron 5 of 7	ENST00000367362.8	NP_995582.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR5A2	ENST00000367362.8	c.1110+24085T>C		intron_variant	Intron 5 of 7	1	NM_205860.3	ENSP00000356331.3
NR5A2	ENST00000236914.7	c.972+24085T>C		intron_variant	Intron 4 of 6	1		ENSP00000236914.3
NR5A2	ENST00000544748.5	c.894+24085T>C		intron_variant	Intron 4 of 6	2		ENSP00000439116.1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43486 AN: 151852 Hom.: 6276 Cov.: 31

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.286 AC: 43497 AN: 151970 Hom.: 6277 Cov.: 31 AF XY: 0.284 AC XY: 21121 AN XY: 74298

African (AFR) AF: 0.287 AC: 11908 AN: 41450

American (AMR) AF: 0.269 AC: 4107 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1282 AN: 3466

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5174

South Asian (SAS) AF: 0.231 AC: 1114 AN: 4816

European-Finnish (FIN) AF: 0.298 AC: 3153 AN: 10570

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19875 AN: 67910

Other (OTH) AF: 0.297 AC: 626 AN: 2108

Alfa AF: 0.294 Hom.: 27834

Bravo AF: 0.285

Asia WGS AF: 0.224 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	14
DANN	Benign	0.63
PhyloP100		1.2
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: rs3828112; hg19: chr1-200042031;