rs1005441851

Variant names:

• chr16-3283832-C-G
• rs1005441851
• NM_005741.5:c.14C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-3283832-C-G
• chr16-3283832-C-T

Variant summary

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

The NM_005741.5(ZNF263):​c.14C>G​(p.Pro5Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,422,778 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P5L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ZNF263 NM_005741.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 0 publications found

Genes affected

ZNF263 (HGNC:13056): (zinc finger protein 263) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and transcription cis-regulatory region binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located 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=0.09264627).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF263	NM_005741.5	c.14C>G	p.Pro5Arg	missense_variant	Exon 1 of 6	ENST00000219069.6	NP_005732.2
ZNF263	NM_001411015.1	c.14C>G	p.Pro5Arg	missense_variant	Exon 1 of 8		NP_001397944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF263	ENST00000219069.6	c.14C>G	p.Pro5Arg	missense_variant	Exon 1 of 6	1	NM_005741.5	ENSP00000219069.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000141 AC: 2 AN: 1422778 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 706142

African (AFR) AF: 0.0000310 AC: 1 AN: 32250

American (AMR) AF: 0.00 AC: 0 AN: 39742

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24282

East Asian (EAS) AF: 0.00 AC: 0 AN: 39026

South Asian (SAS) AF: 0.00 AC: 0 AN: 83198

European-Finnish (FIN) AF: 0.0000220 AC: 1 AN: 45440

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4878

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1095362

Other (OTH) AF: 0.00 AC: 0 AN: 58600

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.097
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	16
DANN	Uncertain	0.98
DEOGEN2	Benign	0.031	T;.;T;.
Eigen	Benign	-0.94
Eigen_PC	Benign	-0.94
FATHMM_MKL	Benign	0.00076	N
LIST_S2	Benign	0.55	T;T;T;T
M_CAP	Benign	0.0034	T
MetaRNN	Benign	0.093	T;T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	1.7	L;.;.;.
PhyloP100		0.059
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-1.1	N;.;.;.
REVEL	Benign	0.016
Sift	Uncertain	0.0040	D;.;.;.
Sift4G	Uncertain	0.052	T;D;D;T
Polyphen		0.16	B;.;.;.
Vest4		0.32
MutPred		0.35		Loss of glycosylation at P5 (P = 0.0156);Loss of glycosylation at P5 (P = 0.0156);Loss of glycosylation at P5 (P = 0.0156);Loss of glycosylation at P5 (P = 0.0156);
MVP		0.13
MPC		0.31
ClinPred		0.39	T
GERP RS		3.1
PromoterAI		-0.057	Neutral
Varity_R		0.047
gMVP		0.51
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: rs1005441851; hg19: chr16-3333832;