16-68566952-G-T

Variant names:

• chr16-68566952-G-T
• rs7118
• ENST00000564558.5:n.*4080G>T

Variant summary

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

The ENST00000564558.5(ZFP90):​n.*4080G>T variant causes a non coding transcript exon 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 ENST00000564558.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 23 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZFP90	NM_001305203.2	c.*2254G>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000563169.7	NP_001292132.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFP90	ENST00000563169.7	c.*2254G>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_001305203.2	ENSP00000454418.2

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

African (AFR) AF: 0.752 AC: 11866 AN: 15788

American (AMR) AF: 0.707 AC: 696 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 3918 AN: 5154

East Asian (EAS) AF: 0.800 AC: 3013 AN: 3768

South Asian (SAS) AF: 0.769 AC: 12652 AN: 16460

European-Finnish (FIN) AF: 0.811 AC: 227 AN: 280

Middle Eastern (MID) AF: 0.759 AC: 1230 AN: 1620

European-Non Finnish (NFE) AF: 0.766 AC: 583922 AN: 761950

Other (OTH) AF: 0.766 AC: 20913 AN: 27298

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

African (AFR) AF: 0.747 AC: 31010 AN: 41486

American (AMR) AF: 0.729 AC: 11130 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2584 AN: 3470

East Asian (EAS) AF: 0.817 AC: 4230 AN: 5180

South Asian (SAS) AF: 0.767 AC: 3690 AN: 4808

European-Finnish (FIN) AF: 0.843 AC: 8931 AN: 10596

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.776 AC: 52738 AN: 67976

Other (OTH) AF: 0.750 AC: 1584 AN: 2112

Alfa AF: 0.763 Hom.: 66500

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
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7118; hg19: chr16-68600855;