rs12331851

Positions:

• chr4-145928143-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.43+10222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0685 in 152,188 control chromosomes in the GnomAD database, including 626 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 0.069 (626 hom., cov: 32)
• Consequence: ZNF827 NM_001306215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF827	NM_001306215.2	c.43+10222C>T		intron_variant		ENST00000508784.6	NP_001293144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF827	ENST00000508784.6	c.43+10222C>T		intron_variant		1	NM_001306215.2	ENSP00000421863.1

Frequencies

GnomAD3 genomes AF: 0.0683 AC: 10391 AN: 152070 Hom.: 621 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0339

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.0136

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0665

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

GnomAD4 genome AF: 0.0685 AC: 10426 AN: 152188 Hom.: 626 Cov.: 32 AF XY: 0.0670 AC XY: 4990 AN XY: 74430

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.0339

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.0378

Gnomad4 SAS AF: 0.0477

Gnomad4 FIN AF: 0.0136

Gnomad4 NFE AF: 0.0310

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0377 Hom.: 217

Bravo AF: 0.0736

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.66

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: rs12331851; hg19: chr4-146849295;