chr2-27621734-T-A

Variant names:

• chr2-27621734-T-A
• rs1881396
• NM_032434.4:c.*273T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032434.4(ZNF512):​c.*273T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ZNF512 NM_032434.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.85
• Publications: 27 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF512	NM_032434.4	c.*273T>A		3_prime_UTR_variant	Exon 14 of 14	ENST00000355467.6	NP_115810.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF512	ENST00000355467.6	c.*273T>A		3_prime_UTR_variant	Exon 14 of 14	2	NM_032434.4	ENSP00000347648.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 184364 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 96752

African (AFR) AF: 0.00 AC: 0 AN: 6428

American (AMR) AF: 0.00 AC: 0 AN: 6464

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5756

East Asian (EAS) AF: 0.00 AC: 0 AN: 11868

South Asian (SAS) AF: 0.00 AC: 0 AN: 21610

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8044

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 748

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 112934

Other (OTH) AF: 0.00 AC: 0 AN: 10512

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 14731

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		2.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs1881396; hg19: chr2-27844601;