rs1944932
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000531398.1(POU2AF1):c.-81+18634A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,938 control chromosomes in the GnomAD database, including 20,035 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 0.50 ( 20035 hom., cov: 31)
Consequence
POU2AF1
ENST00000531398.1 intron
ENST00000531398.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.05
Genes affected
POU2AF1 (HGNC:9211): (POU class 2 homeobox associating factor 1) Enables transcription coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Part of RNA polymerase II transcription regulator complex. [provided by Alliance of Genome Resources, Apr 2022]
BTG4 (HGNC:13862): (BTG anti-proliferation factor 4) The protein encoded by this gene is a member of the BTG/Tob family. This family has structurally related proteins that appear to have antiproliferative properties. This encoded protein can induce G1 arrest in the cell cycle. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BTG4 | XM_024448587.2 | c.663-26563A>T | intron_variant | XP_024304355.1 | ||||
BTG4 | XM_024448588.2 | c.663-26563A>T | intron_variant | XP_024304356.1 | ||||
BTG4 | XM_024448589.2 | c.663-26563A>T | intron_variant | XP_024304357.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POU2AF1 | ENST00000515029.2 | n.53+3707A>T | intron_variant | 1 | ||||||
POU2AF1 | ENST00000531398.1 | c.-81+18634A>T | intron_variant | 4 | ENSP00000433527.1 | |||||
POU2AF1 | ENST00000525890.1 | n.412+23934A>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.498 AC: 75586AN: 151820Hom.: 19976 Cov.: 31
GnomAD3 genomes
AF:
AC:
75586
AN:
151820
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.498 AC: 75707AN: 151938Hom.: 20035 Cov.: 31 AF XY: 0.495 AC XY: 36755AN XY: 74268
GnomAD4 genome
AF:
AC:
75707
AN:
151938
Hom.:
Cov.:
31
AF XY:
AC XY:
36755
AN XY:
74268
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1201
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at