4-145816831-A-T

Position:

• chr4-145816831-A-T

Variant summary

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

The NM_001306215.2(ZNF827):​c.2383+6591T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,126 control chromosomes in the GnomAD database, including 6,914 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 0.29 (6914 hom., cov: 33)
• Consequence: ZNF827 NM_001306215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF827	NM_001306215.2	c.2383+6591T>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.2383+6591T>A		intron_variant		1	NM_001306215.2	ENSP00000421863.1

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44669 AN: 152010 Hom.: 6909 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0778

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.294 AC: 44714 AN: 152126 Hom.: 6914 Cov.: 33 AF XY: 0.285 AC XY: 21194 AN XY: 74354

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.0782

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.292

Alfa AF: 0.164 Hom.: 309

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.68

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: rs878451; hg19: chr4-146737983;