rs9304799

Positions:

• chr19-57693820-T-A

Variant summary

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

The ENST00000596085.1(ZNF551):​c.157+8435T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,154 control chromosomes in the GnomAD database, including 26,313 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 0.58 (26313 hom., cov: 27)
• Consequence: ZNF551 ENST00000596085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 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.157+8435T>A		intron_variant		2		ENSP00000472230

Frequencies

GnomAD3 genomes AF: 0.582 AC: 87971 AN: 151038 Hom.: 26288 Cov.: 27

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.582 AC: 88046 AN: 151154 Hom.: 26313 Cov.: 27 AF XY: 0.576 AC XY: 42544 AN XY: 73798

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.579

Alfa AF: 0.580 Hom.: 3242

Bravo AF: 0.591

Asia WGS AF: 0.471 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
DANN	Benign	0.87

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: rs9304799; hg19: chr19-58205188; COSMIC: COSV56591891; COSMIC: COSV56591891;