19-50051686-A-G

Variant names:

• chr19-50051686-A-G
• rs3097342
• ENST00000601364.5:c.227-1504A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000601364.5(ZNF473):​c.227-1504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 148,836 control chromosomes in the GnomAD database, including 20,757 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 0.49 (20757 hom., cov: 30)
• Consequence: ZNF473 ENST00000601364.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.851
• Publications: 6 publications found

Genes affected

ZNF473 (HGNC:23239): (zinc finger protein 473) This gene encodes a member of the Krueppel C2H2-type zinc-finger family of proteins. The encoded protein, a component of the U7 snRNP complex, plays a role in histone 3'-end pre-mRNA processing and may be required for cell cycle progression to S phase. Expression level and methylation status of this gene may be correlated with bone mineral density. [provided by RefSeq, Jul 2016]

ZNF473CR (HGNC:56021): (ZNF473 cis regulating lncRNA)

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 = 0.589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601364.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF473CR	NR_027257.2		n.606+492A>G		intron	N/A
	ZNF473CR	NR_138096.1		n.606+492A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF473	ENST00000601364.5	TSL:3	c.227-1504A>G		intron	N/A	ENSP00000471595.1
	ZNF473CR	ENST00000527209.1	TSL:2	n.606+492A>G		intron	N/A
	ZNF473CR	ENST00000779692.1		n.321+492A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.492 AC: 73119 AN: 148718 Hom.: 20748 Cov.: 30

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.491 AC: 73143 AN: 148836 Hom.: 20757 Cov.: 30 AF XY: 0.494 AC XY: 35940 AN XY: 72800

African (AFR) AF: 0.295 AC: 11329 AN: 38406

American (AMR) AF: 0.536 AC: 8143 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1653 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1055 AN: 5172

South Asian (SAS) AF: 0.415 AC: 1996 AN: 4810

European-Finnish (FIN) AF: 0.677 AC: 7146 AN: 10558

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40318 AN: 67946

Other (OTH) AF: 0.473 AC: 984 AN: 2082

Alfa AF: 0.327 Hom.: 1122

Bravo AF: 0.464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.9
DANN	Benign	0.61
PhyloP100		0.85
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3097342; hg19: chr19-50554943;