NM_032434.4:c.1395+202G>C

Variant names:

• chr2-27617773-G-C
• rs4666002
• NM_032434.4:c.1395+202G>C

Variant summary

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

The NM_032434.4(ZNF512):​c.1395+202G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,894 control chromosomes in the GnomAD database, including 5,639 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 0.24 (5639 hom., cov: 31)
• Consequence: ZNF512 NM_032434.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 24 publications found

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]

ENSG00000259080 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF512	NM_032434.4	c.1395+202G>C		intron_variant	Intron 13 of 13	ENST00000355467.6	NP_115810.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF512	ENST00000355467.6	c.1395+202G>C		intron_variant	Intron 13 of 13	2	NM_032434.4	ENSP00000347648.3

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36739 AN: 151776 Hom.: 5636 Cov.: 31

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.242 AC: 36750 AN: 151894 Hom.: 5639 Cov.: 31 AF XY: 0.249 AC XY: 18488 AN XY: 74212

African (AFR) AF: 0.0721 AC: 2989 AN: 41442

American (AMR) AF: 0.437 AC: 6666 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1181 AN: 3466

East Asian (EAS) AF: 0.489 AC: 2519 AN: 5156

South Asian (SAS) AF: 0.201 AC: 965 AN: 4812

European-Finnish (FIN) AF: 0.292 AC: 3076 AN: 10518

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18458 AN: 67930

Other (OTH) AF: 0.297 AC: 625 AN: 2106

Alfa AF: 0.256 Hom.: 2988

Bravo AF: 0.249

Asia WGS AF: 0.297 AC: 1035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.34
PhyloP100		0.13
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs4666002; hg19: chr2-27840640;