rs560947

Positions:

• chr16-3135736-T-C

Variant summary

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

The NM_004220.3(ZNF213):​c.-116+349T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,892 control chromosomes in the GnomAD database, including 22,980 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 0.54 (22980 hom., cov: 31)
• Consequence: ZNF213 NM_004220.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

ZNF213 (HGNC:13005): (zinc finger protein 213) C2H2 zinc finger proteins, such as ZNF213, have bipartite structures in which one domain binds DNA or RNA and the other modulates target gene expression.[supplied by OMIM, Apr 2004]

ZNF213-AS1 (HGNC:50505): (ZNF213 antisense RNA 1 (head to head))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF213	NM_004220.3	c.-116+349T>C		intron_variant		ENST00000396878.8	NP_004211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF213	ENST00000396878.8	c.-116+349T>C		intron_variant		1	NM_004220.3	ENSP00000380087.3

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82114 AN: 151776 Hom.: 22974 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.541 AC: 82165 AN: 151892 Hom.: 22980 Cov.: 31 AF XY: 0.539 AC XY: 40024 AN XY: 74212

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.557

Alfa AF: 0.607 Hom.: 37337

Bravo AF: 0.524

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.31

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: rs560947; hg19: chr16-3185737;