2-27592643-A-C

Position:

• chr2-27592643-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032434.4(ZNF512):​c.90-5424A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 126,332 control chromosomes in the GnomAD database, including 5,900 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 0.31 (5900 hom., cov: 23)
• Consequence: ZNF512 NM_032434.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

ZNF512 (HGNC:29380): (zinc finger protein 512) This gene encodes a protein containing four putative zinc finger motifs. Zinc finger motifs may bind to proteins or nucleic acids. Zinc finger-containing proteins are involved in a variety of processes, including regulation of transcription. Alternative splicing results in multiple transcript variants for this gene. [provided by RefSeq, Sep 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF512	NM_032434.4	c.90-5424A>C		intron_variant		ENST00000355467.6	NP_115810.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF512	ENST00000355467.6	c.90-5424A>C		intron_variant		2	NM_032434.4	ENSP00000347648	P3

Frequencies

GnomAD3 genomes AF: 0.310 AC: 39132 AN: 126284 Hom.: 5896 Cov.: 23

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.444

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.310 AC: 39146 AN: 126332 Hom.: 5900 Cov.: 23 AF XY: 0.313 AC XY: 19119 AN XY: 60992

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.363

Alfa AF: 0.268 Hom.: 2674

Bravo AF: 0.289

Asia WGS AF: 0.302 AC: 1053 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.18

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: rs13022873; hg19: chr2-27815510;