rs12553321

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001017363.4(ARID3C):​c.318+361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0346 in 152,138 control chromosomes in the GnomAD database, including 133 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 0.035 ( 133 hom., cov: 32)

Consequence

ARID3C
NM_001017363.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.274
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0975 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARID3CNM_001017363.4 linkuse as main transcriptc.318+361G>A intron_variant ENST00000378909.4
ARID3CNM_001371945.2 linkuse as main transcriptc.318+361G>A intron_variant
ARID3CXM_047422781.1 linkuse as main transcriptc.768+361G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARID3CENST00000378909.4 linkuse as main transcriptc.318+361G>A intron_variant 2 NM_001017363.4 P2
ARID3CENST00000692051.1 linkuse as main transcriptc.318+361G>A intron_variant A2

Frequencies

GnomAD3 genomes
AF:
0.0346
AC:
5260
AN:
152020
Hom.:
134
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0146
Gnomad AMI
AF:
0.0636
Gnomad AMR
AF:
0.0268
Gnomad ASJ
AF:
0.0778
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.105
Gnomad FIN
AF:
0.0434
Gnomad MID
AF:
0.0513
Gnomad NFE
AF:
0.0419
Gnomad OTH
AF:
0.0402
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0346
AC:
5258
AN:
152138
Hom.:
133
Cov.:
32
AF XY:
0.0352
AC XY:
2620
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.0146
Gnomad4 AMR
AF:
0.0267
Gnomad4 ASJ
AF:
0.0778
Gnomad4 EAS
AF:
0.00136
Gnomad4 SAS
AF:
0.105
Gnomad4 FIN
AF:
0.0434
Gnomad4 NFE
AF:
0.0419
Gnomad4 OTH
AF:
0.0393
Alfa
AF:
0.0422
Hom.:
136
Bravo
AF:
0.0302
Asia WGS
AF:
0.0440
AC:
155
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.9
DANN
Benign
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12553321; hg19: chr9-34627333; API