NM_001306215.2:c.2221+1400C>T

Variant names:

• chr4-145847922-G-A
• rs1027841
• NM_001306215.2:c.2221+1400C>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.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
• Publications: 6 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=-0.85).
• 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 rank	MANE	Protein	UniProt
ZNF827	NM_001306215.2	c.2221+1400C>T		intron_variant	Intron 6 of 14	ENST00000508784.6	NP_001293144.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF827	ENST00000508784.6	c.2221+1400C>T		intron_variant	Intron 6 of 14	1	NM_001306215.2	ENSP00000421863.1

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

African (AFR) AF: 0.116 AC: 4833 AN: 41490

American (AMR) AF: 0.366 AC: 5596 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3468

East Asian (EAS) AF: 0.636 AC: 3286 AN: 5168

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1727 AN: 10572

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11304 AN: 67988

Other (OTH) AF: 0.200 AC: 420 AN: 2104

Alfa AF: 0.177 Hom.: 1402

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
PhyloP100		-1.4
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: rs1027841; hg19: chr4-146769074;