rs7198446

chr16-88345763-A-Cchr16-88345763-A-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+69188A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,974 control chromosomes in the GnomAD database, including 18,676 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 (18676 hom., cov: 32)
• Consequence: ZNF469 XM_047434810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

Genes affected

ZNF469 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF469	XM_047434810.1	c.-192+69188A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74341 AN: 151856 Hom.: 18641 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.490 AC: 74412 AN: 151974 Hom.: 18676 Cov.: 32 AF XY: 0.489 AC XY: 36331 AN XY: 74268

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.446

Alfa AF: 0.452 Hom.: 19925

Bravo AF: 0.484

Asia WGS AF: 0.389 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	5.5
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7198446; hg19: chr16-88379369;