2-104855627-CGGCGGGGGCGGCGCAGGG-CGGCGGGGGCGGCGCAGGGGGCGGGGGCGGCGCAGGG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006236.3(POU3F3):​c.131_148dupCAGGGGGCGGGGGCGGCG​(p.Ala44_Gly49dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000175 in 570,352 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 26)
Exomes 𝑓: 0.0000018 ( 0 hom. )

Consequence

POU3F3
NM_006236.3 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.19
Variant links:
Genes affected
POU3F3 (HGNC:9216): (POU class 3 homeobox 3) This gene encodes a POU-domain containing protein that functions as a transcription factor. The encoded protein recognizes an octamer sequence in the DNA of target genes. This protein may play a role in development of the nervous system. [provided by RefSeq, Apr 2015]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
POU3F3NM_006236.3 linkc.131_148dupCAGGGGGCGGGGGCGGCG p.Ala44_Gly49dup disruptive_inframe_insertion Exon 1 of 1 ENST00000361360.4 NP_006227.1 P20264

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
POU3F3ENST00000361360.4 linkc.131_148dupCAGGGGGCGGGGGCGGCG p.Ala44_Gly49dup disruptive_inframe_insertion Exon 1 of 1 6 NM_006236.3 ENSP00000355001.2 P20264

Frequencies

GnomAD3 genomes
Cov.:
26
GnomAD4 exome
AF:
0.00000175
AC:
1
AN:
570352
Hom.:
0
Cov.:
25
AF XY:
0.00
AC XY:
0
AN XY:
264758
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00134
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-105472085; API