chr7-57120141-G-C

Variant names:

• chr7-57120141-G-C
• rs1785846619
• NM_001370129.2:c.1274C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001370129.2(ZNF479):​c.1274C>G​(p.Thr425Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: ZNF479 NM_001370129.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -4.95
• Publications: 0 publications found

Genes affected

ZNF479 (HGNC:23258): (zinc finger protein 479) Predicted to enable DNA-binding transcription factor 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, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.093306184).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370129.2. 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
	ZNF479	NM_001370129.2	MANE Select	c.1274C>G	p.Thr425Ser	missense	Exon 4 of 4	NP_001357058.1	Q96JC4
	ZNF479	NM_033273.3		c.1274C>G	p.Thr425Ser	missense	Exon 5 of 5	NP_150376.1	Q96JC4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF479	ENST00000319636.10	TSL:1 MANE Select	c.1274C>G	p.Thr425Ser	missense	Exon 4 of 4	ENSP00000324518.6	Q96JC4
	ZNF479	ENST00000331162.8	TSL:1	c.1274C>G	p.Thr425Ser	missense	Exon 5 of 5	ENSP00000333776.4	Q96JC4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.42	T
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.67
DEOGEN2	Benign	0.036	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.032	N
LIST_S2	Benign	0.029	T
M_CAP	Benign	0.00049	T
MetaRNN	Benign	0.093	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.34	N
PhyloP100		-5.0
PrimateAI	Benign	0.37	T
PROVEAN	Uncertain	-3.4	D
REVEL	Benign	0.010
Sift	Benign	0.099	T
Sift4G	Benign	0.11	T
Polyphen		0.011	B
Vest4		0.029
MutPred		0.34		Gain of ubiquitination at K428 (P = 0.0762)
MVP		0.17
MPC		0.79
ClinPred		0.041	T
GERP RS		0.89
Varity_R		0.020
gMVP		0.0092
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: rs1785846619; hg19: chr7-57187848;