NM_021224.6:c.-31+6717G>A

Variant names:

• chr9-106870072-G-A
• rs4743034
• NM_021224.6:c.-31+6717G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021224.6(ZNF462):​c.-31+6717G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,078 control chromosomes in the GnomAD database, including 6,307 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 0.27 (6307 hom., cov: 32)
• Consequence: ZNF462 NM_021224.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 47 publications found

Genes affected

ZNF462 (HGNC:21684): (zinc finger protein 462) The protein encoded by this gene belongs to C2H2-type zinc finger family of proteins. It contains multiple C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]

ZNF462 Gene-Disease associations (from GenCC):

• Weiss-Kruszka syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Illumina, Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), PanelApp Australia

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021224.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF462	NM_021224.6	MANE Select	c.-31+6717G>A		intron	N/A	NP_067047.4
	ZNF462	NM_001347997.2		c.-31+6717G>A		intron	N/A	NP_001334926.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF462	ENST00000277225.10	TSL:1 MANE Select	c.-31+6717G>A		intron	N/A	ENSP00000277225.5
	ZNF462	ENST00000472574.1	TSL:4	c.-31+6717G>A		intron	N/A	ENSP00000476222.1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41293 AN: 151958 Hom.: 6281 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.272 AC: 41354 AN: 152078 Hom.: 6307 Cov.: 32 AF XY: 0.270 AC XY: 20038 AN XY: 74338

African (AFR) AF: 0.414 AC: 17156 AN: 41436

American (AMR) AF: 0.189 AC: 2883 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5178

South Asian (SAS) AF: 0.323 AC: 1559 AN: 4822

European-Finnish (FIN) AF: 0.196 AC: 2074 AN: 10564

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15145 AN: 68000

Other (OTH) AF: 0.258 AC: 546 AN: 2114

Alfa AF: 0.238 Hom.: 20731

Bravo AF: 0.275

Asia WGS AF: 0.300 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.16
DANN	Benign	0.50
PhyloP100		-0.53
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: rs4743034; hg19: chr9-109632353;