16-68557327-A-T

Variant names:

• chr16-68557327-A-T
• rs1728785
• NM_001305203.2:c.34-671A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001305203.2(ZFP90):​c.34-671A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000333 in 300,558 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000033 (0 hom.)
• Consequence: ZFP90 NM_001305203.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 86 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001305203.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP90	NM_001305203.2	MANE Select	c.34-671A>T		intron	N/A	NP_001292132.1	Q8TF47-1
	ZFP90	NM_133458.4		c.34-671A>T		intron	N/A	NP_597715.2	Q8TF47-1
	ZFP90	NM_001305204.2		c.34-671A>T		intron	N/A	NP_001292133.1	Q8TF47-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFP90	ENST00000563169.7	TSL:1 MANE Select	c.34-671A>T		intron	N/A	ENSP00000454418.2	Q8TF47-1
	ZFP90	ENST00000570495.5	TSL:1	c.34-671A>T		intron	N/A	ENSP00000460547.1	Q8TF47-1
	ZFP90	ENST00000611381.4	TSL:1	c.34-671A>T		intron	N/A	ENSP00000480309.1	Q8TF47-3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD2 exomes AF: 0.00000784 AC: 1 AN: 127520 AF XY: 0.0000143

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000412

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000333 AC: 1 AN: 300558 Hom.: 0 Cov.: 0 AF XY: 0.00000586 AC XY: 1 AN XY: 170660

African (AFR) AF: 0.00 AC: 0 AN: 8556

American (AMR) AF: 0.0000367 AC: 1 AN: 27216

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10730

East Asian (EAS) AF: 0.00 AC: 0 AN: 9108

South Asian (SAS) AF: 0.00 AC: 0 AN: 59634

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12332

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2772

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 156140

Other (OTH) AF: 0.00 AC: 0 AN: 14070

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.3
DANN	Benign	0.28
PhyloP100		0.32

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: rs1728785; hg19: chr16-68591230;