rs1182968

Positions:

• chr16-68540042-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.33+217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,098 control chromosomes in the GnomAD database, including 44,739 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 (44739 hom., cov: 32)
• Consequence: ZFP90 NM_001305203.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFP90	NM_001305203.2	c.33+217C>T		intron_variant		ENST00000563169.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFP90	ENST00000563169.7	c.33+217C>T		intron_variant		1	NM_001305203.2	P1

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116451 AN: 151980 Hom.: 44714 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.766 AC: 116527 AN: 152098 Hom.: 44739 Cov.: 32 AF XY: 0.768 AC XY: 57129 AN XY: 74368

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.726

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.841

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.746

Alfa AF: 0.766 Hom.: 20559

Bravo AF: 0.758

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.6
DANN	Benign	0.59

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: rs1182968; hg19: chr16-68573945;