1-200048556-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_205860.3(NR5A2):c.848C>T(p.Ser283Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,614,050 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 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 Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR5A2 | ENST00000367362.8 | c.848C>T | p.Ser283Phe | missense_variant | Exon 5 of 8 | 1 | NM_205860.3 | ENSP00000356331.3 | ||
NR5A2 | ENST00000236914.7 | c.710C>T | p.Ser237Phe | missense_variant | Exon 4 of 7 | 1 | ENSP00000236914.3 | |||
NR5A2 | ENST00000367357.3 | c.608C>T | p.Ser203Phe | missense_variant | Exon 3 of 4 | 1 | ENSP00000356326.3 | |||
NR5A2 | ENST00000544748.5 | c.632C>T | p.Ser211Phe | missense_variant | Exon 4 of 7 | 2 | ENSP00000439116.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251356Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135852
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461880Hom.: 1 Cov.: 34 AF XY: 0.0000261 AC XY: 19AN XY: 727240
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.848C>T (p.S283F) alteration is located in exon 5 (coding exon 5) of the NR5A2 gene. This alteration results from a C to T substitution at nucleotide position 848, causing the serine (S) at amino acid position 283 to be replaced by a phenylalanine (F). 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