1-200039721-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_205860.3(NR5A2):c.128C>T(p.Pro43Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,460,112 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_205860.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR5A2 | ENST00000367362.8 | c.128C>T | p.Pro43Leu | missense_variant | Exon 2 of 8 | 1 | NM_205860.3 | ENSP00000356331.3 | ||
NR5A2 | ENST00000447034.1 | c.164C>T | p.Pro55Leu | missense_variant | Exon 3 of 3 | 1 | ENSP00000414888.1 | |||
NR5A2 | ENST00000236914.7 | c.65-4053C>T | intron_variant | Intron 1 of 6 | 1 | ENSP00000236914.3 | ||||
NR5A2 | ENST00000474307.1 | n.*419-4053C>T | intron_variant | Intron 2 of 2 | 1 | ENSP00000436776.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249500Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135122
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460112Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726456
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.128C>T (p.P43L) alteration is located in exon 2 (coding exon 2) of the NR5A2 gene. This alteration results from a C to T substitution at nucleotide position 128, causing the proline (P) at amino acid position 43 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at