chr12-52054441-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000394825.6(NR4A1):c.113C>T(p.Ala38Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000564 in 1,613,720 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000394825.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR4A1 | NM_173157.3 | c.113C>T | p.Ala38Val | missense_variant | 2/7 | ENST00000394825.6 | NP_775180.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR4A1 | ENST00000394825.6 | c.113C>T | p.Ala38Val | missense_variant | 2/7 | 1 | NM_173157.3 | ENSP00000378302 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000375 AC: 57AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250932Hom.: 1 AF XY: 0.000118 AC XY: 16AN XY: 135668
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461454Hom.: 1 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727032
GnomAD4 genome AF: 0.000374 AC: 57AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000604 AC XY: 45AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.152C>T (p.A51V) alteration is located in exon 3 (coding exon 2) of the NR4A1 gene. This alteration results from a C to T substitution at nucleotide position 152, causing the alanine (A) at amino acid position 51 to be replaced by a valine (V). 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