rs76894039

Variant names:

• chr1-200111336-CAAAAAAA-C
• NM_205860.3:c.1230+24_1230+30delAAAAAAA

Your query was ambiguous. Multiple possible variants found:

• chr1-200111336-CAAAAAAA-C
• chr1-200111336-CAAAAAAA-CA
• chr1-200111336-CAAAAAAA-CAA
• chr1-200111336-CAAAAAAA-CAAA
• chr1-200111336-CAAAAAAA-CAAAA
• chr1-200111336-CAAAAAAA-CAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAAAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAAAAAAAAA
• chr1-200111336-CAAAAAAA-CAAAAAAAAAAAAAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_205860.3(NR5A2):​c.1230+24_1230+30delAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000078 in 1,281,362 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 7.8e-7 (0 hom.)
• Consequence: NR5A2 NM_205860.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.987

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR5A2	NM_205860.3	c.1230+24_1230+30delAAAAAAA		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.1230+16_1230+22delAAAAAAA		intron_variant	Intron 6 of 7	1	NM_205860.3	ENSP00000356331.3
NR5A2	ENST00000236914.7	c.1092+16_1092+22delAAAAAAA		intron_variant	Intron 5 of 6	1		ENSP00000236914.3
NR5A2	ENST00000544748.5	c.1014+16_1014+22delAAAAAAA		intron_variant	Intron 5 of 6	2		ENSP00000439116.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 7.80e-7 AC: 1 AN: 1281362 Hom.: 0 AF XY: 0.00000158 AC XY: 1 AN XY: 634170

Gnomad4 AFR exome AF: 0.0000378

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-200080464;