chr1-200048416-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_205860.3(NR5A2):c.708C>A(p.Asp236Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000743 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_205860.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR5A2 | ENST00000367362.8 | c.708C>A | p.Asp236Glu | missense_variant | Exon 5 of 8 | 1 | NM_205860.3 | ENSP00000356331.3 | ||
NR5A2 | ENST00000236914.7 | c.570C>A | p.Asp190Glu | missense_variant | Exon 4 of 7 | 1 | ENSP00000236914.3 | |||
NR5A2 | ENST00000367357.3 | c.468C>A | p.Asp156Glu | missense_variant | Exon 3 of 4 | 1 | ENSP00000356326.3 | |||
NR5A2 | ENST00000544748.5 | c.492C>A | p.Asp164Glu | missense_variant | Exon 4 of 7 | 2 | ENSP00000439116.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251440Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135892
GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461890Hom.: 0 Cov.: 34 AF XY: 0.0000729 AC XY: 53AN XY: 727246
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.708C>A (p.D236E) alteration is located in exon 5 (coding exon 5) of the NR5A2 gene. This alteration results from a C to A substitution at nucleotide position 708, causing the aspartic acid (D) at amino acid position 236 to be replaced by a glutamic acid (E). 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