rs17689437

chr16-68566448-C-T

Variant summary

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

The NM_001305203.2(ZFP90):c.*1750C>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 0.142 in 985,408 control chromosomes in the GnomAD database, including 10,319 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 0.13 (1435 hom., cov: 32)
  • Exomes 𝑓: 0.14 (8884 hom.)
• Consequence: ZFP90 NM_001305203.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFP90	NM_001305203.2	c.*1750C>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.*1750C>T		3_prime_UTR_variant	5/5	1	NM_001305203.2	P1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19920 AN: 152042 Hom.: 1435 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.128

GnomAD4 exome AF: 0.144 AC: 120195 AN: 833246 Hom.: 8884 Cov.: 36 AF XY: 0.144 AC XY: 55566 AN XY: 384790

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.0986

Gnomad4 ASJ exome AF: 0.166

Gnomad4 EAS exome AF: 0.00743

Gnomad4 SAS exome AF: 0.0537

Gnomad4 FIN exome AF: 0.162

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.127

GnomAD4 genome AF: 0.131 AC: 19924 AN: 152162 Hom.: 1435 Cov.: 32 AF XY: 0.130 AC XY: 9635 AN XY: 74384

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.128

Alfa AF: 0.144 Hom.: 3097

Bravo AF: 0.125

Asia WGS AF: 0.0420 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.8
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: rs17689437; hg19: chr16-68600351;