chr5-93584837-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005654.6(NR2F1):c.-187G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 157,960 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.027 ( 94 hom., cov: 30)
Exomes 𝑓: 0.024 ( 7 hom. )
Consequence
NR2F1
NM_005654.6 5_prime_UTR
NM_005654.6 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.795
Genes affected
NR2F1 (HGNC:7975): (nuclear receptor subfamily 2 group F member 1) The protein encoded by this gene is a nuclear hormone receptor and transcriptional regulator. The encoded protein acts as a homodimer and binds to 5'-AGGTCA-3' repeats. Defects in this gene are a cause of Bosch-Boonstra optic atrophy syndrome (BBOAS). [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 5-93584837-G-A is Benign according to our data. Variant chr5-93584837-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 676347.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0273 (4040/148246) while in subpopulation NFE AF= 0.0432 (2875/66474). AF 95% confidence interval is 0.0419. There are 94 homozygotes in gnomad4. There are 1804 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd at 4044 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR2F1 | NM_005654.6 | c.-187G>A | 5_prime_UTR_variant | 1/3 | ENST00000327111.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR2F1 | ENST00000327111.8 | c.-187G>A | 5_prime_UTR_variant | 1/3 | 1 | NM_005654.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0273 AC: 4044AN: 148162Hom.: 94 Cov.: 30
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GnomAD4 exome AF: 0.0236 AC: 229AN: 9714Hom.: 7 Cov.: 2 AF XY: 0.0241 AC XY: 150AN XY: 6216
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GnomAD4 genome ? AF: 0.0273 AC: 4040AN: 148246Hom.: 94 Cov.: 30 AF XY: 0.0250 AC XY: 1804AN XY: 72302
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Cadd
Benign
Dann
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RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at