9-127428858-C-T

Variant names:

• chr9-127428858-C-T
• NM_007135.3:c.43C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_007135.3(ZNF79):​c.43C>T​(p.Pro15Ser) 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. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF79 NM_007135.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.715
• Publications: 0 publications found

Genes affected

ZNF79 (HGNC:13153): (zinc finger protein 79) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.033895522).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007135.3. 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
	ZNF79	NM_007135.3	MANE Select	c.43C>T	p.Pro15Ser	missense	Exon 2 of 5	NP_009066.2	Q15937
	ZNF79	NM_001286696.2		c.-30C>T		5_prime_UTR	Exon 2 of 5	NP_001273625.1	F5H032
	ZNF79	NM_001286697.2		c.-30C>T		5_prime_UTR	Exon 3 of 6	NP_001273626.1	F5H032

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF79	ENST00000342483.5	TSL:1 MANE Select	c.43C>T	p.Pro15Ser	missense	Exon 2 of 5	ENSP00000362446.4	Q15937
	ZNF79	ENST00000850855.1		c.43C>T	p.Pro15Ser	missense	Exon 2 of 3	ENSP00000520943.1	A0ABJ7HDM7
	ZNF79	ENST00000543471.6	TSL:2	c.-30C>T		5_prime_UTR	Exon 3 of 6	ENSP00000438418.1	F5H032

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

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	0.080
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.43
DANN	Benign	0.23
DEOGEN2	Benign	0.093	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.0081	N
LIST_S2	Benign	0.24	T
M_CAP	Benign	0.0023	T
MetaRNN	Benign	0.034	T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.71	N
PhyloP100		-0.71
PrimateAI	Benign	0.41	T
PROVEAN	Benign	0.42	N
REVEL	Benign	0.072
Sift	Benign	0.92	T
Sift4G	Benign	0.28	T
Polyphen		0.0010	B
Vest4		0.050
MutPred		0.21		Gain of phosphorylation at P15 (P = 0.0325)
MVP		0.14
MPC		0.12
ClinPred		0.014	T
GERP RS		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.015
gMVP		0.19
Mutation Taster		=100/0	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

hg19: chr9-130191137;