chr16-88304501-T-C

Position:

• chr16-88304501-T-C

Variant summary

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

The XM_047434810.1(ZNF469):​c.-192+27926T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 151,856 control chromosomes in the GnomAD database, including 31,196 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 0.64 (31196 hom., cov: 30)
• Consequence: ZNF469 XM_047434810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.60

Genes affected

ZNF469 (HGNC:23216): (zinc finger protein 469) This gene encodes a zinc-finger protein. Low-percent homology to certain collagens suggests that it may function as a transcription factor or extra-nuclear regulator factor for the synthesis or organization of collagen fibers. Mutations in this gene cause brittle cornea syndrome. [provided by RefSeq, Jul 2008]

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF469	XM_047434810.1	c.-192+27926T>C		intron_variant			XP_047290766.1
		n.88304501T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97157 AN: 151738 Hom.: 31164 Cov.: 30

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.640 AC: 97237 AN: 151856 Hom.: 31196 Cov.: 30 AF XY: 0.639 AC XY: 47381 AN XY: 74204

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.657

Alfa AF: 0.621 Hom.: 11144

Bravo AF: 0.649

Asia WGS AF: 0.678 AC: 2356 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	0.67
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9925231; hg19: chr16-88338107;