NM_004234.4:c.16-234G>A

Variant names:

• chr19-44299966-C-T
• rs11671074
• NM_004234.4:c.16-234G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004234.4(ZNF235):​c.16-234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,052 control chromosomes in the GnomAD database, including 13,303 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 0.39 (13303 hom., cov: 32)
• Consequence: ZNF235 NM_004234.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 13 publications found

Genes affected

ZNF235 (HGNC:12866): (zinc finger protein 235) This gene product belongs to the zinc finger protein superfamily, members of which are regulatory proteins characterized by nucleic acid-binding zinc finger domains. The encoded protein is a member of the Kruppel family of zinc finger proteins, and contains Kruppel-associated box (KRAB) A and B domains and 15 tandemly arrayed C2H2-type zinc fingers. It is an ortholog of the mouse Zfp93 protein. This gene is located in a cluster of zinc finger genes on 19q13.2. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004234.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF235	NM_004234.4	MANE Select	c.16-234G>A		intron	N/A	NP_004225.3
	ZNF235	NM_001411071.1		c.16-234G>A		intron	N/A	NP_001398000.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF235	ENST00000291182.9	TSL:1 MANE Select	c.16-234G>A		intron	N/A	ENSP00000291182.3
	ZNF235	ENST00000589799.5	TSL:1	c.16-234G>A		intron	N/A	ENSP00000468695.1
	ZNF235	ENST00000650576.1		c.16-234G>A		intron	N/A	ENSP00000497018.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58583 AN: 151934 Hom.: 13303 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.385 AC: 58576 AN: 152052 Hom.: 13303 Cov.: 32 AF XY: 0.388 AC XY: 28873 AN XY: 74322

African (AFR) AF: 0.121 AC: 5022 AN: 41502

American (AMR) AF: 0.440 AC: 6722 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1729 AN: 3466

East Asian (EAS) AF: 0.509 AC: 2634 AN: 5174

South Asian (SAS) AF: 0.578 AC: 2782 AN: 4810

European-Finnish (FIN) AF: 0.439 AC: 4634 AN: 10548

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.493 AC: 33520 AN: 67972

Other (OTH) AF: 0.420 AC: 886 AN: 2108

Alfa AF: 0.454 Hom.: 45693

Bravo AF: 0.370

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.4
DANN	Benign	0.47
PhyloP100		0.33
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: rs11671074; hg19: chr19-44804119;