15-74544324-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_006465.4(ARID3B):āc.388C>Gā(p.Gln130Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,611,920 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006465.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID3B | NM_006465.4 | c.388C>G | p.Gln130Glu | missense_variant | 2/9 | ENST00000346246.10 | |
ARID3B | NM_001307939.2 | c.388C>G | p.Gln130Glu | missense_variant | 2/9 | ||
ARID3B | XR_007064418.1 | n.465C>G | non_coding_transcript_exon_variant | 1/9 | |||
ARID3B | XR_007064419.1 | n.465C>G | non_coding_transcript_exon_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID3B | ENST00000346246.10 | c.388C>G | p.Gln130Glu | missense_variant | 2/9 | 1 | NM_006465.4 | P4 | |
ARID3B | ENST00000622429.1 | c.388C>G | p.Gln130Glu | missense_variant | 2/9 | 1 | A2 | ||
ARID3B | ENST00000569680.1 | n.532C>G | non_coding_transcript_exon_variant | 2/4 | 1 | ||||
ARID3B | ENST00000566147.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000852 AC: 2AN: 234760Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126878
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459700Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 725930
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.388C>G (p.Q130E) alteration is located in exon 2 (coding exon 1) of the ARID3B gene. This alteration results from a C to G substitution at nucleotide position 388, causing the glutamine (Q) at amino acid position 130 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at