11-110124562-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033390.2(ZC3H12C):c.22-12101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,092 control chromosomes in the GnomAD database, including 38,496 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 0.71 (38496 hom., cov: 32)
• Consequence: ZC3H12C NM_033390.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

Genes affected

ZC3H12C (HGNC:29362): (zinc finger CCCH-type containing 12C) Predicted to enable endoribonuclease activity and mRNA binding activity. Predicted to be involved in RNA phosphodiester bond hydrolysis, endonucleolytic. Predicted to be active in cytoplasmic ribonucleoprotein granule and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

RDX (HGNC:9944): (radixin) Radixin is a cytoskeletal protein that may be important in linking actin to the plasma membrane. It is highly similar in sequence to both ezrin and moesin. The radixin gene has been localized by fluorescence in situ hybridization to 11q23. A truncated version representing a pseudogene (RDXP2) was assigned to Xp21.3. Another pseudogene that seemed to lack introns (RDXP1) was mapped to 11p by Southern and PCR analyses. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZC3H12C	NM_033390.2	c.22-12101C>T		intron_variant		ENST00000278590.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZC3H12C	ENST00000278590.8	c.22-12101C>T		intron_variant		2	NM_033390.2
RDX	ENST00000645527.1	c.*546-292G>A		intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107725 AN: 151974 Hom.: 38486 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.697

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.709 AC: 107785 AN: 152092 Hom.: 38496 Cov.: 32 AF XY: 0.703 AC XY: 52243 AN XY: 74338

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.697

Alfa AF: 0.693 Hom.: 73738

Bravo AF: 0.724

Asia WGS AF: 0.715 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.27
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1789369; hg19: chr11-109995287;