rs3810291

chr19-47065746-G-Achr19-47065746-G-C

Variant summary

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

The NM_015168.2(ZC3H4):c.*610C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,596 control chromosomes in the GnomAD database, including 22,476 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 0.50 (22360 hom., cov: 31)
  • Exomes 𝑓: 0.57 (116 hom.)
• Consequence: ZC3H4 NM_015168.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520

Genes affected

ZC3H4 (HGNC:17808): (zinc finger CCCH-type containing 4) This gene encodes a member of a family of CCCH (C-x8-C-x5-C-x3-H type) zinc finger domain-containing proteins. These zinc finger domains, which coordinate zinc finger binding and are characterized by three cysteine residues and one histidine residue, are nucleic acid-binding. Other family members are known to function in post-transcriptional regulation. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZC3H4	NM_015168.2	c.*610C>T		3_prime_UTR_variant	15/15	ENST00000253048.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZC3H4	ENST00000253048.10	c.*610C>T		3_prime_UTR_variant	15/15	1	NM_015168.2	P1
ZC3H4	ENST00000601973.1	c.*610C>T		3_prime_UTR_variant	8/8	5
ZC3H4	ENST00000594019.5	n.2372C>T		non_coding_transcript_exon_variant	7/7	2

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75872 AN: 151848 Hom.: 22358 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.519

GnomAD4 exome AF: 0.575 AC: 362 AN: 630 Hom.: 116 Cov.: 0 AF XY: 0.581 AC XY: 201 AN XY: 346

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.601

Gnomad4 NFE exome AF: 0.657

Gnomad4 OTH exome AF: 0.591

GnomAD4 genome AF: 0.499 AC: 75875 AN: 151966 Hom.: 22360 Cov.: 31 AF XY: 0.496 AC XY: 36865 AN XY: 74270

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.517

Alfa AF: 0.638 Hom.: 45243

Bravo AF: 0.481

Asia WGS AF: 0.358 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.60
Dann	Benign	0.43

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

Other links and lift over

dbSNP: rs3810291; hg19: chr19-47569003;