16-68566952-G-T

Variant summary

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

The NM_001305203.2(ZFP90):c.*2254G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 985,398 control chromosomes in the GnomAD database, including 289,589 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 0.77 (44995 hom., cov: 32)
  • Exomes 𝑓: 0.77 (244594 hom.)
• Consequence: ZFP90 NM_001305203.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

Genes affected

ZFP90 (HGNC:23329): (ZFP90 zinc finger protein) This gene encodes a member of the zinc finger protein family that modulates gene expression. The encoded protein derepresses the transcription of certain fetal cardiac genes and may contribute to the genetic reprogramming that occurs during the development of heart failure. Genome wide association studies have identified this gene among ulcerative colitis risk loci. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Mar 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFP90	NM_001305203.2	c.*2254G>T		3_prime_UTR_variant	5/5	ENST00000563169.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFP90	ENST00000563169.7	c.*2254G>T		3_prime_UTR_variant	5/5	1	NM_001305203.2	P1

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116798 AN: 151978 Hom.: 44971 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.749

GnomAD4 exome AF: 0.766 AC: 638437 AN: 833302 Hom.: 244594 Cov.: 54 AF XY: 0.766 AC XY: 294724 AN XY: 384830

Gnomad4 AFR exome AF: 0.752

Gnomad4 AMR exome AF: 0.707

Gnomad4 ASJ exome AF: 0.760

Gnomad4 EAS exome AF: 0.800

Gnomad4 SAS exome AF: 0.769

Gnomad4 FIN exome AF: 0.811

Gnomad4 NFE exome AF: 0.766

Gnomad4 OTH exome AF: 0.766

GnomAD4 genome AF: 0.768 AC: 116876 AN: 152096 Hom.: 44995 Cov.: 32 AF XY: 0.771 AC XY: 57310 AN XY: 74346

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.750

Alfa AF: 0.761 Hom.: 44326

Bravo AF: 0.760

Asia WGS AF: 0.718 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.8
Dann	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7118; hg19: chr16-68600855;