15-96332202-CCGCCCGG-C
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_021005.4(NR2F2):c.103_109del(p.Gly35ArgfsTer75) variant causes a frameshift change. 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: 6.90
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 Pathogenic. Variant got 12 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 20 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 15-96332202-CCGCCCGG-C is Pathogenic according to our data. Variant chr15-96332202-CCGCCCGG-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 916038.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-96332202-CCGCCCGG-C is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR2F2 | NM_021005.4 | c.103_109del | p.Gly35ArgfsTer75 | frameshift_variant | 1/3 | ENST00000394166.8 | |
NR2F2 | NM_001145155.2 | c.44-1868_44-1862del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR2F2 | ENST00000394166.8 | c.103_109del | p.Gly35ArgfsTer75 | frameshift_variant | 1/3 | 1 | NM_021005.4 | P1 | |
NR2F2 | ENST00000421109.6 | c.44-1868_44-1862del | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
46,xx sex reversal 5 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 02, 2020 | - - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 05, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at