rs4801516

Variant names:

• chr19-57712730-C-T
• rs4801516
• ENST00000594684.1:c.33+30486C>T

Variant summary

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

The ENST00000594684.1(ENSG00000269026):​c.33+30486C>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: ENSG00000269026 ENST00000594684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269026	ENST00000594684.1	c.33+30486C>T		intron_variant	Intron 1 of 2	1		ENSP00000472160.1
ZNF551	ENST00000596085.1	c.158-4437C>T		intron_variant	Intron 2 of 2	2		ENSP00000472230.1
ENSG00000269026	ENST00000599221.1	n.200+30486C>T		intron_variant	Intron 1 of 1	3

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;