chr1-167389600-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002697.4(POU2F1):c.826A>G(p.Thr276Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00303 in 1,614,126 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0031 ( 12 hom. )
Consequence
POU2F1
NM_002697.4 missense
NM_002697.4 missense
Scores
4
6
7
Clinical Significance
Conservation
PhyloP100: 8.91
Genes affected
POU2F1 (HGNC:9212): (POU class 2 homeobox 1) The OCT1 transcription factor was among the first identified members of the POU transcription factor family (summarized by Sturm et al., 1993 [PubMed 8314572]). Members of this family contain the POU domain, a 160-amino acid region necessary for DNA binding to the octameric sequence ATGCAAAT.[supplied by OMIM, Jul 2010]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.010557413).
BP6
?
Variant 1-167389600-A-G is Benign according to our data. Variant chr1-167389600-A-G is described in ClinVar as [Benign]. Clinvar id is 718797.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 371 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POU2F1 | NM_002697.4 | c.826A>G | p.Thr276Ala | missense_variant | 9/16 | ENST00000367866.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU2F1 | ENST00000367866.7 | c.826A>G | p.Thr276Ala | missense_variant | 9/16 | 1 | NM_002697.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00244 AC: 371AN: 152156Hom.: 1 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00304 AC: 765AN: 251324Hom.: 3 AF XY: 0.00310 AC XY: 421AN XY: 135838
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GnomAD4 exome AF: 0.00309 AC: 4515AN: 1461852Hom.: 12 Cov.: 31 AF XY: 0.00294 AC XY: 2140AN XY: 727232
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GnomAD4 genome ? AF: 0.00244 AC: 371AN: 152274Hom.: 1 Cov.: 32 AF XY: 0.00253 AC XY: 188AN XY: 74436
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433
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D
Sift4G
Benign
T;T;T;T;T
Polyphen
0.98, 0.99
.;.;D;D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at