rs4801516

Positions:

• chr19-57712730-C-T

Variant summary

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

The ENST00000596085.1(ZNF551):​c.158-4437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,860 control chromosomes in the GnomAD database, including 20,538 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 0.52 (20538 hom., cov: 31)
• Consequence: ZNF551 ENST00000596085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

Genes affected

ZNF551 (HGNC:25108): (zinc finger protein 551) 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF551	ENST00000596085.1	c.158-4437C>T		intron_variant		2		ENSP00000472230

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78311 AN: 151742 Hom.: 20501 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.516 AC: 78408 AN: 151860 Hom.: 20538 Cov.: 31 AF XY: 0.520 AC XY: 38569 AN XY: 74206

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.533

Alfa AF: 0.482 Hom.: 10092

Bravo AF: 0.519

Asia WGS AF: 0.524 AC: 1821 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.58

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: rs4801516; hg19: chr19-58224098;