16-88287830-C-T

Position:

• chr16-88287830-C-T

Variant summary

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

The XM_047434810.1(ZNF469):​c.-192+11255C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,068 control chromosomes in the GnomAD database, including 40,137 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 0.72 (40137 hom., cov: 32)
• Consequence: ZNF469 XM_047434810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

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]

ENSG00000261273 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF469	XM_047434810.1	c.-192+11255C>T		intron_variant			XP_047290766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000261273	ENST00000563190.1	n.222-6889C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109552 AN: 151950 Hom.: 40078 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.721 AC: 109669 AN: 152068 Hom.: 40137 Cov.: 32 AF XY: 0.722 AC XY: 53692 AN XY: 74340

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.713

Alfa AF: 0.693 Hom.: 16562

Bravo AF: 0.736

Asia WGS AF: 0.802 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6540223; hg19: chr16-88321436;