rs750310776

Variant names:

• chr19-48285917-C-A
• rs750310776
• NM_153608.4:c.293C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-48285917-C-A
• chr19-48285917-C-T

Variant summary

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

The NM_153608.4(ZNF114):​c.293C>A​(p.Pro98Gln) 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. 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. P98L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF114 NM_153608.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 0 publications found

Genes affected

ZNF114 (HGNC:12894): (zinc finger protein 114) Enables identical protein binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ZNF114-AS1 (HGNC:53930): (ZNF114 antisense RNA 1)

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=0.068728864).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153608.4. 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
	ZNF114	NM_153608.4	MANE Select	c.293C>A	p.Pro98Gln	missense	Exon 6 of 6	NP_705836.1	Q8NC26-1
	ZNF114	NM_001331098.1		c.431C>A	p.Pro144Gln	missense	Exon 6 of 6	NP_001318027.1
	ZNF114	NM_001331097.1		c.293C>A	p.Pro98Gln	missense	Exon 6 of 6	NP_001318026.1	Q8NC26-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF114	ENST00000595607.6	TSL:1 MANE Select	c.293C>A	p.Pro98Gln	missense	Exon 6 of 6	ENSP00000469998.1	Q8NC26-1
	ZNF114	ENST00000315849.5	TSL:2	c.293C>A	p.Pro98Gln	missense	Exon 5 of 5	ENSP00000318898.1	Q8NC26-1
	ZNF114	ENST00000600687.5	TSL:5	c.293C>A	p.Pro98Gln	missense	Exon 5 of 5	ENSP00000471727.1	Q8NC26-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.31
DEOGEN2	Benign	0.011	T
Eigen	Benign	-0.90
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.050	N
LIST_S2	Benign	0.42	T
M_CAP	Benign	0.0018	T
MetaRNN	Benign	0.069	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.34
PrimateAI	Benign	0.25	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.080
Sift	Benign	0.83	T
Sift4G	Benign	0.77	T
Polyphen		0.96	D
Vest4		0.14
MutPred		0.12		Gain of MoRF binding (P = 0.1082)
MVP		0.31
MPC		0.63
ClinPred		0.15	T
GERP RS		-0.40
Varity_R		0.031
gMVP		0.077
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

dbSNP: rs750310776; hg19: chr19-48789174;