rs7500421

chr16-88330877-T-G

Variant summary

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

The XM_047434810.1(ZNF469):c.-192+54302T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,092 control chromosomes in the GnomAD database, including 3,717 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 0.22 (3717 hom., cov: 33)
• Consequence: ZNF469 XM_047434810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

ZNF469 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF469	XM_047434810.1	c.-192+54302T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33069 AN: 151974 Hom.: 3696 Cov.: 33

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.218 AC: 33125 AN: 152092 Hom.: 3717 Cov.: 33 AF XY: 0.217 AC XY: 16163 AN XY: 74354

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.201

Alfa AF: 0.225 Hom.: 5306

Bravo AF: 0.210

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.25
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7500421; hg19: chr16-88364483;