rs8101149

chr19-47097184-G-A

Variant summary

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

The NM_015168.2(ZC3H4):c.162-2576C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,094 control chromosomes in the GnomAD database, including 24,559 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 0.52 (24559 hom., cov: 33)
• Consequence: ZC3H4 NM_015168.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZC3H4	NM_015168.2	c.162-2576C>T		intron_variant		ENST00000253048.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZC3H4	ENST00000253048.10	c.162-2576C>T		intron_variant		1	NM_015168.2	P1
ZC3H4	ENST00000594019.5	n.83-2576C>T		intron_variant, non_coding_transcript_variant		2
ZC3H4	ENST00000597069.1	n.163-2576C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79635 AN: 151976 Hom.: 24558 Cov.: 33

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.524 AC: 79637 AN: 152094 Hom.: 24559 Cov.: 33 AF XY: 0.521 AC XY: 38701 AN XY: 74344

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.536

Alfa AF: 0.614 Hom.: 6416

Bravo AF: 0.505

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.012
Dann	Benign	0.36

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: rs8101149; hg19: chr19-47600441;