rs1556974668

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chrX-153420300-C-G
• chrX-153420300-C-T

Variant summary

Our verdict is Likely benign. Variant got -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. 12/18 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

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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.036556542).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFP92	NM_001136273.2	c.233C>G	p.Pro78Arg	missense_variant	Exon 5 of 6	ENST00000338647.7	NP_001129745.1
ZFP92	NM_001386944.1	c.233C>G	p.Pro78Arg	missense_variant	Exon 4 of 5		NP_001373873.1
ZFP92	NM_001386945.1	c.233C>G	p.Pro78Arg	missense_variant	Exon 6 of 7		NP_001373874.1
ZFP92	NM_001386943.1	c.107C>G	p.Pro36Arg	missense_variant	Exon 3 of 4		NP_001373872.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFP92	ENST00000338647.7	c.233C>G	p.Pro78Arg	missense_variant	Exon 5 of 6	5	NM_001136273.2	ENSP00000462054.1

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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
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

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-152685758;