rs1027841

Positions:

• chr4-145847922-G-A

Variant summary

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

The NM_001306215.2(ZNF827):​c.2221+1400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,106 control chromosomes in the GnomAD database, including 3,918 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 0.19 (3918 hom., cov: 32)
• Consequence: ZNF827 NM_001306215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF827	NM_001306215.2	c.2221+1400C>T		intron_variant		ENST00000508784.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF827	ENST00000508784.6	c.2221+1400C>T		intron_variant		1	NM_001306215.2

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29205 AN: 151988 Hom.: 3912 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.192 AC: 29221 AN: 152106 Hom.: 3918 Cov.: 32 AF XY: 0.200 AC XY: 14875 AN XY: 74352

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.200

Alfa AF: 0.178 Hom.: 1282

Bravo AF: 0.205

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.55

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: rs1027841; hg19: chr4-146769074;