X-153420300-C-G

Variant names:

• chrX-153420300-C-G
• rs1556974668
• NM_001136273.2:c.233C>G

Variant summary

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

The NM_001136273.2(ZFP92):​c.233C>G​(p.Pro78Arg) 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. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P78L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 24)
• Consequence: ZFP92 NM_001136273.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• 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: 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=0.036556542).

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.233C>G	p.Pro78Arg	missense	Exon 5 of 6	NP_001129745.1	A6NM28
	ZFP92	NM_001386944.1		c.233C>G	p.Pro78Arg	missense	Exon 4 of 5	NP_001373873.1	A6NM28
	ZFP92	NM_001386945.1		c.233C>G	p.Pro78Arg	missense	Exon 6 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.233C>G	p.Pro78Arg	missense	Exon 5 of 6	ENSP00000462054.1	A6NM28
	ZFP92	ENST00000881745.1		c.233C>G	p.Pro78Arg	missense	Exon 4 of 5	ENSP00000551804.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.63	T
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0040
DANN	Benign	0.73
DEOGEN2	Benign	0.027	T
FATHMM_MKL	Benign	0.0024	N
LIST_S2	Benign	0.17	T
M_CAP	Benign	0.0017	T
MetaRNN	Benign	0.037	T
MutationAssessor	Benign	-0.81	N
PhyloP100		-1.8
PrimateAI	Benign	0.24	T
Sift4G	Benign	0.12	T
Polyphen		0.0	B
Vest4		0.046
MVP		0.043
MPC		1.1
GERP RS		-5.3
Varity_R		0.048
gMVP		0.16
Mutation Taster		=99/1	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: rs1556974668; hg19: chrX-152685758;