rs9304799

Variant names:

• chr19-57693820-T-A
• rs9304799
• ENST00000594684.1:c.33+11576T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000594684.1(ENSG00000269026):​c.33+11576T>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: ENSG00000269026 ENST00000594684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 3 publications found

Genes affected

ENSG00000269026 (HGNC:):

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269026	ENST00000594684.1	c.33+11576T>A		intron_variant	Intron 1 of 2	1		ENSP00000472160.1
ZNF551	ENST00000596085.1	c.157+8435T>A		intron_variant	Intron 2 of 2	2		ENSP00000472230.1
ENSG00000269026	ENST00000599221.1	n.200+11576T>A		intron_variant	Intron 1 of 1	3

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

African (AFR) AF: 0.694 AC: 28550 AN: 41118

American (AMR) AF: 0.465 AC: 7055 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2093 AN: 3464

East Asian (EAS) AF: 0.533 AC: 2716 AN: 5092

South Asian (SAS) AF: 0.347 AC: 1656 AN: 4770

European-Finnish (FIN) AF: 0.546 AC: 5711 AN: 10452

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38291 AN: 67796

Other (OTH) AF: 0.579 AC: 1215 AN: 2098

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
PhyloP100		-0.41
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: rs9304799; hg19: chr19-58205188; COSMIC: COSV56591891; COSMIC: COSV56591891;