19-58255802-T-C

Position:

• chr19-58255802-T-C

Variant summary

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

The NM_014480.4(ZNF544):​c.245-5049T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 152,100 control chromosomes in the GnomAD database, including 27,452 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 0.60 (27452 hom., cov: 33)
• Consequence: ZNF544 NM_014480.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

ZNF544 (HGNC:16759): (zinc finger protein 544) Predicted to enable DNA-binding transcription activator 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]

ENSG00000283515 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF544	NM_014480.4	c.245-5049T>C		intron_variant		ENST00000687789.1	NP_055295.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF544	ENST00000687789.1	c.245-5049T>C		intron_variant			NM_014480.4	ENSP00000510489.1
ENSG00000283515	ENST00000637233.1	n.209+9008T>C		intron_variant		5		ENSP00000490395.1

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90806 AN: 151982 Hom.: 27416 Cov.: 33

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.598 AC: 90889 AN: 152100 Hom.: 27452 Cov.: 33 AF XY: 0.600 AC XY: 44574 AN XY: 74344

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.601

Alfa AF: 0.588 Hom.: 4458

Bravo AF: 0.606

Asia WGS AF: 0.541 AC: 1880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.4
DANN	Benign	0.54

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: rs260454; hg19: chr19-58767168;