rs13283357
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001017363.4(ARID3C):c.72G>A(p.Pro24=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 1,551,502 control chromosomes in the GnomAD database, including 91,190 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 0.28 ( 6821 hom., cov: 33)
Exomes 𝑓: 0.34 ( 84369 hom. )
Consequence
ARID3C
NM_001017363.4 synonymous
NM_001017363.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00300
Genes affected
ARID3C (HGNC:21209): (AT-rich interaction domain 3C) This gene is a member of the ARID (AT-rich interaction domain) family of proteins. The ARID domain is a helix-turn-helix motif-based DNA-binding domain. ARID family members 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 Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP7
?
Synonymous conserved (PhyloP=0.003 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID3C | NM_001017363.4 | c.72G>A | p.Pro24= | synonymous_variant | 2/8 | ENST00000378909.4 | |
ARID3C | NM_001371945.2 | c.72G>A | p.Pro24= | synonymous_variant | 2/7 | ||
ARID3C | XM_047422781.1 | c.522G>A | p.Pro174= | synonymous_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID3C | ENST00000378909.4 | c.72G>A | p.Pro24= | synonymous_variant | 2/8 | 2 | NM_001017363.4 | P2 | |
ARID3C | ENST00000692051.1 | c.72G>A | p.Pro24= | synonymous_variant | 2/6 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.277 AC: 42190AN: 152064Hom.: 6818 Cov.: 33
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GnomAD3 exomes AF: 0.279 AC: 42582AN: 152848Hom.: 6899 AF XY: 0.277 AC XY: 22628AN XY: 81716
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GnomAD4 exome AF: 0.337 AC: 471554AN: 1399320Hom.: 84369 Cov.: 36 AF XY: 0.333 AC XY: 230092AN XY: 690302
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GnomAD4 genome ? AF: 0.277 AC: 42208AN: 152182Hom.: 6821 Cov.: 33 AF XY: 0.270 AC XY: 20083AN XY: 74416
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at