19-44299966-C-T

Position:

• chr19-44299966-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF235	NM_004234.4	c.16-234G>A		intron_variant		ENST00000291182.9	NP_004225.3
ZNF235	NM_001411071.1	c.16-234G>A		intron_variant			NP_001398000.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF235	ENST00000291182.9	c.16-234G>A		intron_variant		1	NM_004234.4	ENSP00000291182	P4

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

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.420

Alfa AF: 0.481 Hom.: 30532

Bravo AF: 0.370

Asia WGS AF: 0.514 AC: 1787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.4
DANN	Benign	0.47

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: rs11671074; hg19: chr19-44804119;