20-63958981-C-T

Variant names:

• chr20-63958981-C-T
• rs817321
• NM_020713.3:c.*907G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF512B	NM_020713.3	c.*907G>A		3_prime_UTR_variant	Exon 17 of 17	ENST00000369888.6	NP_065764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF512B	ENST00000369888.6	c.*907G>A		3_prime_UTR_variant	Exon 17 of 17	1	NM_020713.3	ENSP00000358904.1

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

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8

East Asian (EAS) AF: 0.00 AC: 0 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 12

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.00843 AC: 3 AN: 356

Other (OTH) AF: 0.0714 AC: 1 AN: 14

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

African (AFR) AF: 0.0678 AC: 2817 AN: 41530

American (AMR) AF: 0.0215 AC: 329 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00864 AC: 30 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00228 AC: 11 AN: 4822

European-Finnish (FIN) AF: 0.00489 AC: 52 AN: 10624

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0111 AC: 756 AN: 68024

Other (OTH) AF: 0.0351 AC: 74 AN: 2110

Alfa AF: 0.0141 Hom.: 67

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
PhyloP100		-0.081
Mutation Taster		=100/0	polymorphism

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: rs817321; hg19: chr20-62590334;