chr19-37424252-G-A

Position:

• chr19-37424252-G-A

Variant summary

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

The NM_152484.3(ZNF569):​c.238+1616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 152,136 control chromosomes in the GnomAD database, including 545 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 0.070 (545 hom., cov: 31)
• Consequence: ZNF569 NM_152484.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587

Genes affected

ZNF569 (HGNC:24737): (zinc finger protein 569) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF569	NM_152484.3	c.238+1616C>T		intron_variant		ENST00000316950.11	NP_689697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF569	ENST00000316950.11	c.238+1616C>T		intron_variant		1	NM_152484.3	ENSP00000325018.5

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10665 AN: 152018 Hom.: 546 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0615

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0353

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0701 AC: 10670 AN: 152136 Hom.: 545 Cov.: 31 AF XY: 0.0703 AC XY: 5227 AN XY: 74360

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.0305

Gnomad4 EAS AF: 0.0865

Gnomad4 SAS AF: 0.0216

Gnomad4 FIN AF: 0.0615

Gnomad4 NFE AF: 0.0353

Gnomad4 OTH AF: 0.0729

Alfa AF: 0.0185 Hom.: 12

Bravo AF: 0.0767

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7255938; hg19: chr19-37915154;