4-145932013-A-G

Variant names:

• chr4-145932013-A-G
• rs2048161
• NM_001306215.2:c.43+6352T>C

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+6352T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.931 in 152,190 control chromosomes in the GnomAD database, including 66,056 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 0.93 (66056 hom., cov: 30)
• Consequence: ZNF827 NM_001306215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 8 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF827	NM_001306215.2	c.43+6352T>C		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+6352T>C		intron_variant	Intron 1 of 14	1	NM_001306215.2	ENSP00000421863.1

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141515 AN: 152072 Hom.: 65994 Cov.: 30

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.931 AC: 141637 AN: 152190 Hom.: 66056 Cov.: 30 AF XY: 0.934 AC XY: 69453 AN XY: 74386

African (AFR) AF: 0.978 AC: 40583 AN: 41512

American (AMR) AF: 0.916 AC: 14013 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3026 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5171 AN: 5174

South Asian (SAS) AF: 0.982 AC: 4725 AN: 4812

European-Finnish (FIN) AF: 0.960 AC: 10168 AN: 10594

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 60980 AN: 68016

Other (OTH) AF: 0.909 AC: 1921 AN: 2114

Alfa AF: 0.910 Hom.: 166061

Bravo AF: 0.929

Asia WGS AF: 0.986 AC: 3430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		0.24
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: rs2048161; hg19: chr4-146853165;