chr19-37424252-G-A

Variant names:

• chr19-37424252-G-A
• rs7255938
• NM_152484.3:c.238+1616C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152484.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF569	NM_152484.3	MANE Select	c.238+1616C>T		intron	N/A	NP_689697.2
	ZNF569	NM_001330482.2		c.-239-9833C>T		intron	N/A	NP_001317411.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF569	ENST00000316950.11	TSL:1 MANE Select	c.238+1616C>T		intron	N/A	ENSP00000325018.5
	ZNF569	ENST00000392149.6	TSL:1	c.238+1616C>T		intron	N/A	ENSP00000375992.2
	ZNF569	ENST00000392150.2	TSL:1	c.-239-9833C>T		intron	N/A	ENSP00000375993.2

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

African (AFR) AF: 0.133 AC: 5514 AN: 41504

American (AMR) AF: 0.0841 AC: 1284 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3472

East Asian (EAS) AF: 0.0865 AC: 447 AN: 5168

South Asian (SAS) AF: 0.0216 AC: 104 AN: 4820

European-Finnish (FIN) AF: 0.0615 AC: 650 AN: 10572

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0353 AC: 2400 AN: 68008

Other (OTH) AF: 0.0729 AC: 154 AN: 2112

Alfa AF: 0.0238 Hom.: 18

Bravo AF: 0.0767

Asia WGS AF: 0.0670 AC: 232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7255938; hg19: chr19-37915154;