chr19-47097184-G-A

Variant names:

• chr19-47097184-G-A
• rs8101149
• NM_015168.2:c.162-2576C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015168.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZC3H4	NM_015168.2	MANE Select	c.162-2576C>T		intron	N/A	NP_055983.1	Q9UPT8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZC3H4	ENST00000253048.10	TSL:1 MANE Select	c.162-2576C>T		intron	N/A	ENSP00000253048.4	Q9UPT8
	ZC3H4	ENST00000594019.5	TSL:2	n.83-2576C>T		intron	N/A
	ZC3H4	ENST00000597069.1	TSL:4	n.163-2576C>T		intron	N/A

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

African (AFR) AF: 0.203 AC: 8410 AN: 41490

American (AMR) AF: 0.559 AC: 8536 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2178 AN: 3462

East Asian (EAS) AF: 0.281 AC: 1454 AN: 5170

South Asian (SAS) AF: 0.424 AC: 2045 AN: 4822

European-Finnish (FIN) AF: 0.651 AC: 6881 AN: 10568

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48239 AN: 67980

Other (OTH) AF: 0.536 AC: 1134 AN: 2116

Alfa AF: 0.600 Hom.: 11092

Bravo AF: 0.505

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.012
DANN	Benign	0.36
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8101149; hg19: chr19-47600441;