NM_001271458.2:c.102+300T>G

Variant names:

• chr11-111300921-T-G
• rs3802840
• NM_001271458.2:c.102+300T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001271458.2(POU2AF3):​c.102+300T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,120 control chromosomes in the GnomAD database, including 38,329 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.71 (38329 hom., cov: 33)
• Consequence: POU2AF3 NM_001271458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 11 publications found

Genes affected

POU2AF3 (HGNC:26978): (POU class 2 homeobox associating factor 3) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

COLCA1 (HGNC:33789): (colorectal cancer associated 1) This gene encodes a transmembrane protein that localizes to granular structures, including crystalloid eosinophilic granules and other granular organelles. This gene, along with an overlapping opposite strand gene, has been implicated as a susceptibility locus for colorectal cancer. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271458.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2AF3	NM_001271458.2	MANE Select	c.102+300T>G		intron	N/A	NP_001258387.1
	POU2AF3	NM_001136105.3		c.-190+300T>G		intron	N/A	NP_001129577.1
	POU2AF3	NM_001271457.2		c.-190+300T>G		intron	N/A	NP_001258386.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2AF3	ENST00000610738.6	TSL:1 MANE Select	c.102+300T>G		intron	N/A	ENSP00000484135.1
	POU2AF3	ENST00000638573.1	TSL:1	c.207+300T>G		intron	N/A	ENSP00000492570.1
	POU2AF3	ENST00000398035.6	TSL:1	c.-190+300T>G		intron	N/A	ENSP00000381115.2

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107608 AN: 152002 Hom.: 38294 Cov.: 33

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.712

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.708 AC: 107693 AN: 152120 Hom.: 38329 Cov.: 33 AF XY: 0.712 AC XY: 52916 AN XY: 74360

African (AFR) AF: 0.654 AC: 27135 AN: 41482

American (AMR) AF: 0.777 AC: 11890 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2517 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5158

South Asian (SAS) AF: 0.828 AC: 3989 AN: 4818

European-Finnish (FIN) AF: 0.773 AC: 8184 AN: 10588

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48671 AN: 67978

Other (OTH) AF: 0.716 AC: 1515 AN: 2116

Alfa AF: 0.712 Hom.: 50431

Bravo AF: 0.701

Asia WGS AF: 0.758 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		-1.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs3802840; hg19: chr11-111171646;