19-58294671-A-G

Position:

• chr19-58294671-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000621650.2(ZNF8):​c.863A>G​(p.Lys288Arg) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZNF8 ENST00000621650.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -2.49

Genes affected

ZNF8 (HGNC:13154): (zinc finger protein 8) 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 negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within BMP signaling pathway. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000283515 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16548029).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF8	NM_021089.3	c.863A>G	p.Lys288Arg	missense_variant	4/4	ENST00000621650.2	NP_066575.2
ZNF8-ERVK3-1	NR_144447.1	n.2441A>G		non_coding_transcript_exon_variant	4/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF8	ENST00000621650.2	c.863A>G	p.Lys288Arg	missense_variant	4/4	1	NM_021089.3	ENSP00000477716.1
ENSG00000283515	ENST00000637233.1	n.*787A>G		non_coding_transcript_exon_variant	9/12	5		ENSP00000490395.1
ENSG00000283515	ENST00000637233.1	n.*787A>G		3_prime_UTR_variant	9/12	5		ENSP00000490395.1
ZNF8-ERVK3-1	ENST00000591325.1	n.2441A>G		non_coding_transcript_exon_variant	4/7	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 16, 2021

The c.863A>G (p.K288R) alteration is located in exon 4 (coding exon 4) of the ZNF8 gene. This alteration results from a A to G substitution at nucleotide position 863, causing the lysine (K) at amino acid position 288 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	20
DANN	Uncertain	1.0
DEOGEN2	Benign	0.051	T
Eigen	Benign	0.091
Eigen_PC	Benign	0.071
FATHMM_MKL	Benign	0.23	N
LIST_S2	Benign	0.14	T
M_CAP	Benign	0.0065	T
MetaRNN	Benign	0.17	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.14	N
MutationTaster	Benign	1.0	N
PrimateAI	Benign	0.47	T
Sift4G	Benign	0.094	T
Polyphen		0.98	D
Vest4		0.16
MutPred		0.34		Loss of methylation at K288 (P = 9e-04);
MVP		0.35
ClinPred		0.62	D
GERP RS		4.8
Varity_R		0.092
gMVP		0.041

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: chr19-58806037;