rs560947

Variant names:

• chr16-3135736-T-C
• rs560947
• NM_004220.3:c.-116+349T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZNF213	NM_004220.3	c.-116+349T>C		intron_variant	Intron 1 of 5	ENST00000396878.8	NP_004211.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF213	ENST00000396878.8	c.-116+349T>C		intron_variant	Intron 1 of 5	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

African (AFR) AF: 0.434 AC: 17982 AN: 41424

American (AMR) AF: 0.493 AC: 7535 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2130 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1233 AN: 5164

South Asian (SAS) AF: 0.599 AC: 2873 AN: 4796

European-Finnish (FIN) AF: 0.585 AC: 6155 AN: 10520

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42293 AN: 67936

Other (OTH) AF: 0.557 AC: 1172 AN: 2106

Alfa AF: 0.600 Hom.: 48159

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
PhyloP100		-0.086
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: rs560947; hg19: chr16-3185737;