3-23962081-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005126.5(NR1D2):c.622C>A(p.Gln208Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005126.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR1D2 | NM_005126.5 | c.622C>A | p.Gln208Lys | missense_variant | Exon 5 of 8 | ENST00000312521.9 | NP_005117.3 | |
NR1D2 | NM_001145425.2 | c.397C>A | p.Gln133Lys | missense_variant | Exon 5 of 8 | NP_001138897.1 | ||
NR1D2 | XM_006713451.4 | c.622C>A | p.Gln208Lys | missense_variant | Exon 5 of 7 | XP_006713514.1 | ||
NR1D2 | NR_110524.2 | n.915C>A | non_coding_transcript_exon_variant | Exon 5 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR1D2 | ENST00000312521.9 | c.622C>A | p.Gln208Lys | missense_variant | Exon 5 of 8 | 1 | NM_005126.5 | ENSP00000310006.3 | ||
NR1D2 | ENST00000383773.8 | n.622C>A | non_coding_transcript_exon_variant | Exon 5 of 9 | 1 | ENSP00000373283.3 | ||||
NR1D2 | ENST00000468700.1 | n.626C>A | non_coding_transcript_exon_variant | Exon 4 of 4 | 3 | |||||
NR1D2 | ENST00000492552.5 | n.739C>A | non_coding_transcript_exon_variant | Exon 5 of 8 | 2 | ENSP00000520893.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251188Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135782
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727232
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.622C>A (p.Q208K) alteration is located in exon 5 (coding exon 5) of the NR1D2 gene. This alteration results from a C to A substitution at nucleotide position 622, causing the glutamine (Q) at amino acid position 208 to be replaced by a lysine (K). 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