4-145829814-C-T

Position:

• chr4-145829814-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001306215.2(ZNF827):​c.2280-6289G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,002 control chromosomes in the GnomAD database, including 6,991 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6991 hom., cov: 32)
• Consequence: ZNF827 NM_001306215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.621

Genes affected

ZNF827 (HGNC:27193): (zinc finger protein 827) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF827 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF827	NM_001306215.2	c.2280-6289G>A		intron_variant		ENST00000508784.6	NP_001293144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF827	ENST00000508784.6	c.2280-6289G>A		intron_variant		1	NM_001306215.2	ENSP00000421863.1

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41881 AN: 151884 Hom.: 6982 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.800

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.272

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.276 AC: 41910 AN: 152002 Hom.: 6991 Cov.: 32 AF XY: 0.287 AC XY: 21286 AN XY: 74296

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.800

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.275

Alfa AF: 0.248 Hom.: 10901

Bravo AF: 0.289

Asia WGS AF: 0.561 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.6
DANN	Benign	0.72

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

LitVar

Other links and lift over

dbSNP: rs13149290; hg19: chr4-146750966;