chr15-74591254-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_006465.4(ARID3B):c.985C>T(p.Pro329Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000248 in 1,613,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
ARID3B
NM_006465.4 missense
NM_006465.4 missense
Scores
2
6
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.75
Genes affected
ARID3B (HGNC:14350): (AT-rich interaction domain 3B) This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA-binding proteins. The encoded protein is homologous with two proteins that bind to the retinoblastoma gene product, and also with the mouse Bright and Drosophila dead ringer proteins. A pseudogene on chromosome 1p31 exists for this gene. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant where missense usually causes diseases, ARID3B
BP4
Computational evidence support a benign effect (MetaRNN=0.3243143).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID3B | NM_006465.4 | c.985C>T | p.Pro329Ser | missense_variant | 6/9 | ENST00000346246.10 | |
ARID3B | NM_001307939.2 | c.985C>T | p.Pro329Ser | missense_variant | 6/9 | ||
ARID3B | XR_007064418.1 | n.1062C>T | non_coding_transcript_exon_variant | 5/9 | |||
ARID3B | XR_007064419.1 | n.1062C>T | non_coding_transcript_exon_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID3B | ENST00000346246.10 | c.985C>T | p.Pro329Ser | missense_variant | 6/9 | 1 | NM_006465.4 | P4 | |
ARID3B | ENST00000622429.1 | c.985C>T | p.Pro329Ser | missense_variant | 6/9 | 1 | A2 | ||
ARID3B | ENST00000566468.1 | n.68C>T | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
ARID3B | ENST00000566147.1 | c.262C>T | p.Pro88Ser | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461668Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727136
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;.;D
REVEL
Benign
Sift
Benign
T;.;T
Sift4G
Benign
T;T;T
Polyphen
D;P;.
Vest4
MutPred
Gain of phosphorylation at P329 (P = 0.0023);Gain of phosphorylation at P329 (P = 0.0023);.;
MVP
MPC
ClinPred
D
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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