19-44428797-C-G

Variant names:

• chr19-44428797-C-G
• rs1434579
• NM_014518.4:c.1984G>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_014518.4(ZNF229):​c.1984G>C​(p.Gly662Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF229 NM_014518.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 0 publications found

Genes affected

ZNF229 (HGNC:13022): (zinc finger protein 229) Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF229 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ENSG00000267188 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014518.4. 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
	ZNF229	NM_014518.4	MANE Select	c.1984G>C	p.Gly662Arg	missense	Exon 6 of 6	NP_055333.3
	ZNF229	NM_001278510.3		c.1966G>C	p.Gly656Arg	missense	Exon 6 of 6	NP_001265439.2
	ZNF229	NR_103551.3		n.2868G>C		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF229	ENST00000614049.5	TSL:1 MANE Select	c.1984G>C	p.Gly662Arg	missense	Exon 6 of 6	ENSP00000479884.1
	ZNF229	ENST00000613197.4	TSL:1	c.1966G>C	p.Gly656Arg	missense	Exon 6 of 6	ENSP00000479807.1
	ZNF229	ENST00000620012.4	TSL:1	n.*2187G>C		non_coding_transcript_exon	Exon 6 of 6	ENSP00000483138.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 83

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.49
BayesDel_addAF	Benign	-0.046	T
BayesDel_noAF	Benign	-0.30
CADD	Benign	22
DANN	Uncertain	1.0
Eigen	Benign	0.089
Eigen_PC	Benign	-0.15
FATHMM_MKL	Benign	0.73	D
LIST_S2	Benign	0.85	T
M_CAP	Benign	0.011	T
MetaRNN	Uncertain	0.56	D
MetaSVM	Uncertain	0.080	D
PhyloP100		1.7
PrimateAI	Uncertain	0.49	T
Sift4G	Uncertain	0.011	D
Vest4		0.091
MutPred		0.64		Gain of MoRF binding (P = 0.0186)
MVP		0.71
ClinPred		0.89	D
GERP RS		3.5
gMVP		0.053
Mutation Taster		=97/3	polymorphism

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: rs1434579; hg19: chr19-44932972;