rs817321

Positions:

• chr20-63958981-C-T

Variant summary

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

The NM_020713.3(ZNF512B):​c.*907G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 152,686 control chromosomes in the GnomAD database, including 100 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 0.027 (100 hom., cov: 33)
  • Exomes 𝑓: 0.012 (0 hom.)
• Consequence: ZNF512B NM_020713.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

Genes affected

ZNF512B (HGNC:29212): (zinc finger protein 512B) Predicted to enable DNA binding activity and metal ion binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF512B	NM_020713.3	c.*907G>A		3_prime_UTR_variant	17/17	ENST00000369888.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF512B	ENST00000369888.6	c.*907G>A		3_prime_UTR_variant	17/17	1	NM_020713.3	P1

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4102 AN: 152144 Hom.: 99 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00249

Gnomad FIN AF: 0.00489

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0354

GnomAD4 exome AF: 0.0118 AC: 5 AN: 424 Hom.: 0 Cov.: 0 AF XY: 0.0123 AC XY: 4 AN XY: 326

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00843

Gnomad4 OTH exome AF: 0.0714

GnomAD4 genome AF: 0.0270 AC: 4107 AN: 152262 Hom.: 100 Cov.: 33 AF XY: 0.0255 AC XY: 1900 AN XY: 74438

Gnomad4 AFR AF: 0.0678

Gnomad4 AMR AF: 0.0215

Gnomad4 ASJ AF: 0.00864

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.00489

Gnomad4 NFE AF: 0.0111

Gnomad4 OTH AF: 0.0351

Alfa AF: 0.0140 Hom.: 30

Bravo AF: 0.0297

Asia WGS AF: 0.00491 AC: 17 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.46

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: rs817321; hg19: chr20-62590334;