rs3802842

Positions:

• chr11-111300984-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001271458.2(POU2AF3):​c.102+363C>A 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 152,100 control chromosomes in the GnomAD database, including 38,312 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 (38312 hom., cov: 32)
• Consequence: POU2AF3 NM_001271458.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POU2AF3	NM_001271458.2	c.102+363C>A		intron_variant		ENST00000610738.6
COLCA1	NR_169237.1	n.222-2318G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU2AF3	ENST00000610738.6	c.102+363C>A		intron_variant		1	NM_001271458.2	P2
COLCA1	ENST00000620864.1	n.219-2318G>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107574 AN: 151982 Hom.: 38276 Cov.: 32

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: 0.827

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.708 AC: 107660 AN: 152100 Hom.: 38312 Cov.: 32 AF XY: 0.711 AC XY: 52893 AN XY: 74342

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.716

Alfa AF: 0.714 Hom.: 89602

Bravo AF: 0.701

Asia WGS AF: 0.758 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3802842; hg19: chr11-111171709;