rs2288539
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_005234.4(NR2F6):c.318C>T(p.Asn106=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,613,984 control chromosomes in the GnomAD database, including 17,082 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 2445 hom., cov: 33)
Exomes 𝑓: 0.13 ( 14637 hom. )
Consequence
NR2F6
NM_005234.4 synonymous
NM_005234.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.30
Genes affected
NR2F6 (HGNC:7977): (nuclear receptor subfamily 2 group F member 6) Enables DNA-binding transcription factor activity and sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP7
?
Synonymous conserved (PhyloP=3.3 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR2F6 | NM_005234.4 | c.318C>T | p.Asn106= | synonymous_variant | 2/4 | ENST00000291442.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR2F6 | ENST00000291442.4 | c.318C>T | p.Asn106= | synonymous_variant | 2/4 | 1 | NM_005234.4 | P1 | |
NR2F6 | ENST00000596878.1 | c.-43C>T | 5_prime_UTR_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.163 AC: 24846AN: 152068Hom.: 2438 Cov.: 33
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GnomAD3 exomes AF: 0.170 AC: 42628AN: 251344Hom.: 4833 AF XY: 0.163 AC XY: 22102AN XY: 135848
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GnomAD4 exome AF: 0.129 AC: 188533AN: 1461798Hom.: 14637 Cov.: 32 AF XY: 0.131 AC XY: 95024AN XY: 727212
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GnomAD4 genome ? AF: 0.163 AC: 24878AN: 152186Hom.: 2445 Cov.: 33 AF XY: 0.165 AC XY: 12286AN XY: 74404
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Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at