rs1213851181

Variant names:

• chr2-104855612-TGGCGGCGGCGGCGGC-T
• NM_006236.3:c.108_122delCGGCGGCGGCGGCGG

Your query was ambiguous. Multiple possible variants found:

• chr2-104855612-TGGCGGCGGCGGCGGC-T
• chr2-104855612-TGGCGGCGGCGGCGGC-TGGC
• chr2-104855612-TGGCGGCGGCGGCGGC-TGGCGGC
• chr2-104855612-TGGCGGCGGCGGCGGC-TGGCGGCGGC
• chr2-104855612-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGC
• chr2-104855612-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGC
• chr2-104855612-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGC
• chr2-104855612-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGC
• chr2-104855612-TGGCGGCGGCGGCGGC-TGGCGGCGGCGGCGGCGGCGGCGGCGGCGGC

Variant summary

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

The NM_006236.3(POU3F3):​c.108_122delCGGCGGCGGCGGCGG​(p.Gly37_Gly41del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000161 in 619,800 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: 20)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: POU3F3 NM_006236.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.82

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]

ENSG00000269707 (HGNC:):

ACMG classification

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
POU3F3	NM_006236.3	c.108_122delCGGCGGCGGCGGCGG	p.Gly37_Gly41del	disruptive_inframe_deletion	Exon 1 of 1	ENST00000361360.4	NP_006227.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POU3F3	ENST00000361360.4	c.108_122delCGGCGGCGGCGGCGG	p.Gly37_Gly41del	disruptive_inframe_deletion	Exon 1 of 1	6	NM_006236.3	ENSP00000355001.2

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome AF: 0.00000161 AC: 1 AN: 619800 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 287972

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

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: 0.00000177

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: chr2-105472070;