3-23956113-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_005126.5(NR1D2):c.360C>T(p.Cys120Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00533 in 1,612,538 control chromosomes in the GnomAD database, including 399 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.027 ( 211 hom., cov: 33)
Exomes 𝑓: 0.0031 ( 188 hom. )
Consequence
NR1D2
NM_005126.5 synonymous
NM_005126.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.43
Genes affected
NR1D2 (HGNC:7963): (nuclear receptor subfamily 1 group D member 2) This gene encodes a member of the nuclear hormone receptor family, specifically the NR1 subfamily of receptors. The encoded protein functions as a transcriptional repressor and may play a role in circadian rhythms and carbohydrate and lipid metabolism. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 3-23956113-C-T is Benign according to our data. Variant chr3-23956113-C-T is described in ClinVar as [Benign]. Clinvar id is 775851.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.43 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0911 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR1D2 | NM_005126.5 | c.360C>T | p.Cys120Cys | synonymous_variant | Exon 3 of 8 | ENST00000312521.9 | NP_005117.3 | |
NR1D2 | NM_001145425.2 | c.135C>T | p.Cys45Cys | synonymous_variant | Exon 3 of 8 | NP_001138897.1 | ||
NR1D2 | XM_006713451.4 | c.360C>T | p.Cys120Cys | synonymous_variant | Exon 3 of 7 | XP_006713514.1 | ||
NR1D2 | NR_110524.2 | n.653C>T | non_coding_transcript_exon_variant | Exon 3 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR1D2 | ENST00000312521.9 | c.360C>T | p.Cys120Cys | synonymous_variant | Exon 3 of 8 | 1 | NM_005126.5 | ENSP00000310006.3 | ||
NR1D2 | ENST00000383773.8 | n.360C>T | non_coding_transcript_exon_variant | Exon 3 of 9 | 1 | ENSP00000373283.3 | ||||
NR1D2 | ENST00000468700.1 | n.255C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | |||||
NR1D2 | ENST00000492552.5 | n.477C>T | non_coding_transcript_exon_variant | Exon 3 of 8 | 2 | ENSP00000520893.1 |
Frequencies
GnomAD3 genomes AF: 0.0271 AC: 4121AN: 152036Hom.: 211 Cov.: 33
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GnomAD3 exomes AF: 0.00752 AC: 1891AN: 251460Hom.: 85 AF XY: 0.00558 AC XY: 759AN XY: 135900
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GnomAD4 exome AF: 0.00306 AC: 4475AN: 1460384Hom.: 188 Cov.: 29 AF XY: 0.00269 AC XY: 1955AN XY: 726602
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GnomAD4 genome AF: 0.0271 AC: 4125AN: 152154Hom.: 211 Cov.: 33 AF XY: 0.0265 AC XY: 1972AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at