NM_001136273.2:c.943A>G

Variant names:

• chrX-153421320-A-G
• NM_001136273.2:c.943A>G

Variant summary

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

The NM_001136273.2(ZFP92):​c.943A>G​(p.Ser315Gly) 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. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 26)
• Consequence: ZFP92 NM_001136273.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.353
• Publications: 0 publications found

Genes affected

ZFP92 (HGNC:12865): (ZFP92 zinc finger protein) 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 by RNA polymerase II. Predicted to be active 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=0.18953034).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136273.2. 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
	ZFP92	NM_001136273.2	MANE Select	c.943A>G	p.Ser315Gly	missense	Exon 6 of 6	NP_001129745.1	A6NM28
	ZFP92	NM_001386944.1		c.943A>G	p.Ser315Gly	missense	Exon 5 of 5	NP_001373873.1	A6NM28
	ZFP92	NM_001386945.1		c.943A>G	p.Ser315Gly	missense	Exon 7 of 7	NP_001373874.1	A6NM28

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP92	ENST00000338647.7	TSL:5 MANE Select	c.943A>G	p.Ser315Gly	missense	Exon 6 of 6	ENSP00000462054.1	A6NM28
	ZFP92	ENST00000881745.1		c.943A>G	p.Ser315Gly	missense	Exon 5 of 5	ENSP00000551804.1

Frequencies

GnomAD3 genomes Cov.: 26

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 26

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	0.14
BayesDel_addAF	Benign	-0.46	T
BayesDel_noAF	Benign	-0.89
CADD	Benign	19
DANN	Benign	0.74
DEOGEN2	Benign	0.12	T
FATHMM_MKL	Benign	0.44	N
LIST_S2	Benign	0.46	T
M_CAP	Benign	0.032	D
MetaRNN	Benign	0.19	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.35
PrimateAI	Uncertain	0.63	T
Sift4G	Pathogenic	0.0010	D
Polyphen		0.94	P
Vest4		0.073
MVP		0.34
MPC		1.8
GERP RS		1.9
Varity_R		0.059
gMVP		0.49
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

hg19: chrX-152686778;