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rs3802842

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.580
Variant links:
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]

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ACMG classification

Classification made for transcript

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
POU2AF3NM_001271458.2 linkuse as main transcriptc.102+363C>A intron_variant ENST00000610738.6
COLCA1NR_169237.1 linkuse as main transcriptn.222-2318G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
POU2AF3ENST00000610738.6 linkuse as main transcriptc.102+363C>A intron_variant 1 NM_001271458.2 P2A8K830-5
COLCA1ENST00000620864.1 linkuse as main transcriptn.219-2318G>T intron_variant, non_coding_transcript_variant 1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3802842; hg19: chr11-111171709; API