chr3-23954593-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005126.5(NR1D2):c.73C>T(p.His25Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H25L) has been classified 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR1D2 | NM_005126.5 | c.73C>T | p.His25Tyr | missense_variant | Exon 2 of 8 | ENST00000312521.9 | NP_005117.3 | |
NR1D2 | XM_006713451.4 | c.73C>T | p.His25Tyr | missense_variant | Exon 2 of 7 | XP_006713514.1 | ||
NR1D2 | NM_001145425.2 | c.-153C>T | 5_prime_UTR_variant | Exon 2 of 8 | NP_001138897.1 | |||
NR1D2 | NR_110524.2 | n.366C>T | non_coding_transcript_exon_variant | Exon 2 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR1D2 | ENST00000312521.9 | c.73C>T | p.His25Tyr | missense_variant | Exon 2 of 8 | 1 | NM_005126.5 | ENSP00000310006.3 | ||
NR1D2 | ENST00000383773.8 | n.73C>T | non_coding_transcript_exon_variant | Exon 2 of 9 | 1 | ENSP00000373283.3 | ||||
NR1D2 | ENST00000492552.5 | n.190C>T | non_coding_transcript_exon_variant | Exon 2 of 8 | 2 | ENSP00000520893.1 | ||||
NR1D2 | ENST00000468700.1 | n.-33C>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251454Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135898
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461676Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727164
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.73C>T (p.H25Y) alteration is located in exon 2 (coding exon 2) of the NR1D2 gene. This alteration results from a C to T substitution at nucleotide position 73, causing the histidine (H) at amino acid position 25 to be replaced by a tyrosine (Y). 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