rs10800666

Variant names:

• chr1-200104602-A-C
• rs10800666
• NM_205860.3:c.1111-6600A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-200104602-A-C
• chr1-200104602-A-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.1111-6600A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,018 control chromosomes in the GnomAD database, including 15,572 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 0.45 (15572 hom., cov: 32)
• Consequence: NR5A2 NM_205860.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• 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]

LOC107985244 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR5A2	NM_205860.3	MANE Select	c.1111-6600A>C		intron	N/A	NP_995582.1
	NR5A2	NM_003822.5		c.973-6600A>C		intron	N/A	NP_003813.1
	NR5A2	NM_001276464.2		c.895-6600A>C		intron	N/A	NP_001263393.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR5A2	ENST00000367362.8	TSL:1 MANE Select	c.1111-6600A>C		intron	N/A	ENSP00000356331.3
	NR5A2	ENST00000236914.7	TSL:1	c.973-6600A>C		intron	N/A	ENSP00000236914.3
	NR5A2	ENST00000544748.5	TSL:2	c.895-6600A>C		intron	N/A	ENSP00000439116.1

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68273 AN: 151900 Hom.: 15541 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.450 AC: 68347 AN: 152018 Hom.: 15572 Cov.: 32 AF XY: 0.443 AC XY: 32915 AN XY: 74294

African (AFR) AF: 0.486 AC: 20158 AN: 41478

American (AMR) AF: 0.472 AC: 7213 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1531 AN: 5156

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4820

European-Finnish (FIN) AF: 0.393 AC: 4145 AN: 10548

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30522 AN: 67970

Other (OTH) AF: 0.453 AC: 953 AN: 2104

Alfa AF: 0.317 Hom.: 758

Bravo AF: 0.455

Asia WGS AF: 0.376 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.79
PhyloP100		0.31
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: rs10800666; hg19: chr1-200073730; COSMIC: COSV52647299;