dbSNP rs1430848259: POU3F3:p.Gly41_Gly43del (chr2-104855624-CGGCGGCGGG-C) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_006236.3(POU3F3):c.122_130delGGGGCGGCG(p.Gly41_Gly43del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 758,138 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000037 ( 0 hom., cov: 6)

Exomes 𝑓: 0.000015 ( 0 hom. )

Consequence

POU3F3
NM_006236.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.65

Publications

0 publications found

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]

POU3F3 links:

ENSG00000269707 (HGNC:):

ENSG00000269707 links:

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]

PANTR1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP6

Variant 2-104855624-CGGCGGCGGG-C is Benign according to our data. Variant chr2-104855624-CGGCGGCGGG-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2358994.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAdExome4 at 10 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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
POU3F3	NM_006236.3	MANE Select	c.122_130delGGGGCGGCG	p.Gly41_Gly43del	disruptive_inframe_deletion	Exon 1 of 1	NP_006227.1	P20264
POU3F3	NM_001433704.1		c.122_130delGGGGCGGCG	p.Gly41_Gly43del	disruptive_inframe_deletion	Exon 2 of 2	NP_001420633.1	P20264
POU3F3	NR_197431.1		n.294+2063_294+2071delGGGGCGGCG		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
POU3F3	ENST00000361360.4	TSL:6 MANE Select	c.122_130delGGGGCGGCG	p.Gly41_Gly43del	disruptive_inframe_deletion	Exon 1 of 1	ENSP00000355001.2	P20264
POU3F3	ENST00000674056.1		c.122_130delGGGGCGGCG	p.Gly41_Gly43del	disruptive_inframe_deletion	Exon 4 of 4	ENSP00000501036.1	P20264
ENSG00000269707	ENST00000598623.1	TSL:5	n.345+1800_345+1808delGGGGCGGCG		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000367

AC:

AN:

81704

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000794

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000247

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000148

AC:

AN:

676436

Hom.:

AF XY:

0.00000956

AC XY:

AN XY:

313718

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

12970

American (AMR)

AF:

0.00

AC:

AN:

798

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4234

East Asian (EAS)

AF:

0.00

AC:

AN:

3088

South Asian (SAS)

AF:

0.00

AC:

AN:

14000

European-Finnish (FIN)

AF:

0.00

AC:

AN:

294

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1306

European-Non Finnish (NFE)

AF:

0.0000162

AC:

AN:

617480

Other (OTH)

AF:

0.00

AC:

AN:

22266

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000367

AC:

AN:

81702

Hom.:

Cov.:

AF XY:

0.0000508

AC XY:

AN XY:

39368

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

22004

American (AMR)

AF:

0.00

AC:

AN:

7526

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2202

East Asian (EAS)

AF:

0.000797

AC:

AN:

2508

South Asian (SAS)

AF:

0.00

AC:

AN:

2186

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3036

Middle Eastern (MID)

AF:

0.00

AC:

AN:

130

European-Non Finnish (NFE)

AF:

0.0000247

AC:

AN:

40478

Other (OTH)

AF:

0.00

AC:

AN:

1108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.6

Mutation Taster

=191/9

polymorphism

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over