rs1303053833

Variant names:

• chr2-104855630-CGGG-C
• rs1303053833
• NM_006236.3:c.123_125delGGG

Your query was ambiguous. Multiple possible variants found:

• chr2-104855630-CGGG-C
• chr2-104855630-CGGG-CGG
• chr2-104855630-CGGG-CGGGGGG

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_006236.3(POU3F3):​c.123_125delGGG​(p.Gly42del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000024 in 291,540 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: 0.000024 (0 hom.)
• Consequence: POU3F3 NM_006236.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 0 publications found

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:):

PANTR1 (HGNC:49513): (POU3F3 adjacent non-coding transcript 1) Predicted to act upstream of or within regulation of gene expression. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 7 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006236.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU3F3	NM_006236.3	MANE Select	c.123_125delGGG	p.Gly42del	disruptive_inframe_deletion	Exon 1 of 1	NP_006227.1	P20264
	POU3F3	NM_001433704.1		c.123_125delGGG	p.Gly42del	disruptive_inframe_deletion	Exon 2 of 2	NP_001420633.1	P20264
	POU3F3	NR_197431.1		n.294+2064_294+2066delGGG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU3F3	ENST00000361360.4	TSL:6 MANE Select	c.123_125delGGG	p.Gly42del	disruptive_inframe_deletion	Exon 1 of 1	ENSP00000355001.2	P20264
	POU3F3	ENST00000674056.1		c.123_125delGGG	p.Gly42del	disruptive_inframe_deletion	Exon 4 of 4	ENSP00000501036.1	P20264
	ENSG00000269707	ENST00000598623.1	TSL:5	n.345+1801_345+1803delGGG		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome AF: 0.0000240 AC: 7 AN: 291540 Hom.: 0 AF XY: 0.0000296 AC XY: 4 AN XY: 135228

African (AFR) AF: 0.000174 AC: 1 AN: 5750

American (AMR) AF: 0.00 AC: 0 AN: 430

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1804

East Asian (EAS) AF: 0.00 AC: 0 AN: 1462

South Asian (SAS) AF: 0.00 AC: 0 AN: 6156

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 154

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 554

European-Non Finnish (NFE) AF: 0.0000226 AC: 6 AN: 265688

Other (OTH) AF: 0.00 AC: 0 AN: 9542

GnomAD4 genome Cov.: 26

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1303053833; hg19: chr2-105472088;