rs1110061
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004959.5(NR5A1):c.437G>T(p.Gly146Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,455,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G146A) has been classified as Benign.
Frequency
Consequence
NM_004959.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR5A1 | NM_004959.5 | c.437G>T | p.Gly146Val | missense_variant | 4/7 | ENST00000373588.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR5A1 | ENST00000373588.9 | c.437G>T | p.Gly146Val | missense_variant | 4/7 | 1 | NM_004959.5 | P1 | |
NR5A1 | ENST00000620110.4 | c.437G>T | p.Gly146Val | missense_variant | 4/6 | 5 | |||
NR5A1 | ENST00000455734.1 | c.437G>T | p.Gly146Val | missense_variant | 4/4 | 3 | |||
NR5A1 | ENST00000373587.3 | c.40-251G>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000428 AC: 1AN: 233592Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129032
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1455312Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 724024
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at