chr15-96332186-G-GCC
Position:
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_021005.4(NR2F2):c.83_84dup(p.Val29ProfsTer84) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 31)
Consequence
NR2F2
NM_021005.4 frameshift
NM_021005.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.86
Genes affected
NR2F2 (HGNC:7976): (nuclear receptor subfamily 2 group F member 2) This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 5 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 15-96332186-G-GCC is Pathogenic according to our data. Variant chr15-96332186-G-GCC is described in ClinVar as [Likely_pathogenic]. Clinvar id is 547880.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR2F2 | NM_021005.4 | c.83_84dup | p.Val29ProfsTer84 | frameshift_variant | 1/3 | ENST00000394166.8 | NP_066285.1 | |
NR2F2 | NM_001145155.2 | c.44-1888_44-1887dup | intron_variant | NP_001138627.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR2F2 | ENST00000394166.8 | c.83_84dup | p.Val29ProfsTer84 | frameshift_variant | 1/3 | 1 | NM_021005.4 | ENSP00000377721 | P1 | |
NR2F2 | ENST00000421109.6 | c.44-1888_44-1887dup | intron_variant | 1 | ENSP00000401674 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital heart defects, multiple types, 4 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Nov 07, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at