chr4-145928143-G-A

Variant names:

• chr4-145928143-G-A
• rs12331851
• NM_001306215.2:c.43+10222C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF827	NM_001306215.2	c.43+10222C>T		intron_variant	Intron 1 of 14	ENST00000508784.6	NP_001293144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF827	ENST00000508784.6	c.43+10222C>T		intron_variant	Intron 1 of 14	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

African (AFR) AF: 0.164 AC: 6803 AN: 41472

American (AMR) AF: 0.0339 AC: 518 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3472

East Asian (EAS) AF: 0.0378 AC: 196 AN: 5186

South Asian (SAS) AF: 0.0477 AC: 230 AN: 4820

European-Finnish (FIN) AF: 0.0136 AC: 144 AN: 10614

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0310 AC: 2107 AN: 68016

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

Alfa AF: 0.0395 Hom.: 561

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
PhyloP100		-0.032
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12331851; hg19: chr4-146849295;