rs10410711

chr19-36449796-A-G

Variant summary

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

The NM_001145344.1(ZNF566):c.438T>C(p.His146=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 1,614,094 control chromosomes in the GnomAD database, including 981 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 0.036 (138 hom., cov: 32)
  • Exomes 𝑓: 0.027 (843 hom.)
• Consequence: ZNF566 NM_001145344.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

Genes affected

ZNF566 (HGNC:25919): (zinc finger protein 566) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Predicted to be integral component of membrane. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZNF566	NM_001145344.1	c.438T>C	p.His146=	synonymous_variant	5/5	ENST00000452939.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZNF566	ENST00000452939.7	c.438T>C	p.His146=	synonymous_variant	5/5	2	NM_001145344.1	P4

Frequencies

GnomAD3 genomes AF: 0.0361 AC: 5490 AN: 152134 Hom.: 136 Cov.: 32

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0212

Gnomad ASJ AF: 0.0502

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0208

Gnomad OTH AF: 0.0354

GnomAD3 exomes AF: 0.0329 AC: 8271 AN: 251396 Hom.: 264 AF XY: 0.0318 AC XY: 4317 AN XY: 135864

Gnomad AFR exome AF: 0.0596

Gnomad AMR exome AF: 0.0153

Gnomad ASJ exome AF: 0.0512

Gnomad EAS exome AF: 0.128

Gnomad SAS exome AF: 0.0240

Gnomad FIN exome AF: 0.0252

Gnomad NFE exome AF: 0.0214

Gnomad OTH exome AF: 0.0307

GnomAD4 exome AF: 0.0272 AC: 39756 AN: 1461842 Hom.: 843 Cov.: 31 AF XY: 0.0271 AC XY: 19685 AN XY: 727220

Gnomad4 AFR exome AF: 0.0641

Gnomad4 AMR exome AF: 0.0155

Gnomad4 ASJ exome AF: 0.0548

Gnomad4 EAS exome AF: 0.138

Gnomad4 SAS exome AF: 0.0235

Gnomad4 FIN exome AF: 0.0241

Gnomad4 NFE exome AF: 0.0221

Gnomad4 OTH exome AF: 0.0324

GnomAD4 genome AF: 0.0362 AC: 5504 AN: 152252 Hom.: 138 Cov.: 32 AF XY: 0.0361 AC XY: 2685 AN XY: 74446

Gnomad4 AFR AF: 0.0602

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.0502

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.0208

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0256 Hom.: 109

Bravo AF: 0.0381

Asia WGS AF: 0.0760 AC: 262 AN: 3478

EpiCase AF: 0.0236

EpiControl AF: 0.0235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.31

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: rs10410711; hg19: chr19-36940698; COSMIC: COSV67574376; COSMIC: COSV67574376;