rs2195980

Variant names:

• chr19-43847542-C-A
• rs2195980
• NM_181845.2:c.941C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-43847542-C-A
• chr19-43847542-C-T

Variant summary

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

The ENST00000618787.5(ZNF283):​c.941C>A​(p.Thr314Asn) 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. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 29)
• Consequence: ZNF283 ENST00000618787.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 28 publications found

Genes affected

ZNF283 (HGNC:13077): (zinc finger protein 283) 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=0.09462112).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000618787.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF283	NM_181845.2	MANE Select	c.941C>A	p.Thr314Asn	missense	Exon 7 of 7	NP_862828.1
	ZNF283	NM_001297752.2		c.524C>A	p.Thr175Asn	missense	Exon 6 of 6	NP_001284681.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF283	ENST00000618787.5	TSL:2 MANE Select	c.941C>A	p.Thr314Asn	missense	Exon 7 of 7	ENSP00000484852.1
	ZNF283	ENST00000324461.9	TSL:1	c.941C>A	p.Thr314Asn	missense	Exon 4 of 4	ENSP00000327314.7
	ZNF283	ENST00000650832.1		c.833C>A	p.Thr278Asn	missense	Exon 7 of 7	ENSP00000498705.1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 75

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 24010

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	17
DANN	Uncertain	0.98
DEOGEN2	Benign	0.035	T
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.71
FATHMM_MKL	Benign	0.037	N
LIST_S2	Benign	0.039	T
M_CAP	Benign	0.0049	T
MetaRNN	Benign	0.095	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.2	L
PhyloP100		0.55
PrimateAI	Benign	0.37	T
PROVEAN	Uncertain	-3.2	D
REVEL	Benign	0.029
Sift	Uncertain	0.0030	D
Sift4G	Uncertain	0.027	D
Polyphen		0.0010	B
Vest4		0.18
MutPred		0.36		Gain of MoRF binding (P = 0.1155)
MVP		0.24
MPC		0.35
ClinPred		0.58	D
GERP RS		2.0
Varity_R		0.28
gMVP		0.021
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: rs2195980; hg19: chr19-44351694;