chr16-88264518-C-T

Position:

• chr16-88264518-C-T

Variant summary

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

The XM_047435026.1(LOC124900374):​c.-468G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 145,808 control chromosomes in the GnomAD database, including 22,729 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 0.53 (22729 hom., cov: 21)
• Consequence: LOC124900374 XM_047435026.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

LOC124900374 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900374	XM_047435026.1	c.-468G>A		5_prime_UTR_premature_start_codon_gain_variant	1/2		XP_047290982.1
LOC124900374	XM_047435026.1	c.-468G>A		5_prime_UTR_variant	1/2		XP_047290982.1
ZNF469	XM_047434810.1	c.-293-11956C>T		intron_variant			XP_047290766.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000261273	ENST00000563190.1	n.120-11956C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.534 AC: 77792 AN: 145690 Hom.: 22712 Cov.: 21

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.534 AC: 77828 AN: 145808 Hom.: 22729 Cov.: 21 AF XY: 0.532 AC XY: 37633 AN XY: 70690

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.580

Alfa AF: 0.625 Hom.: 48598

Bravo AF: 0.533

Asia WGS AF: 0.610 AC: 2112 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12447690; hg19: chr16-88298124;