dbSNP rs17689437: ZFP90:n.*3576C>T (chr16-68566448-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000564558.5(ZFP90):n.*3576C>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 0.142 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
ENST00000564558.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Publications

22 publications found

Variant links:

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]

ZFP90 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZFP90	NM_001305203.2 link	c.*1750C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000563169.7	NP_001292132.1	Q8TF47-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFP90	ENST00000563169.7 link	c.*1750C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_001305203.2	ENSP00000454418.2		Q8TF47-1

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19920

AN:

152042

Hom.:

1435

Cov.:

show subpopulations

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.:

AF XY:

0.144

AC XY:

55566

AN XY:

384790

show subpopulations

African (AFR)

AF:

0.114

AC:

1806

AN:

15786

American (AMR)

AF:

0.0986

AC:

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

855

AN:

5152

East Asian (EAS)

AF:

0.00743

AC:

AN:

3770

South Asian (SAS)

AF:

0.0537

AC:

884

AN:

16460

European-Finnish (FIN)

AF:

0.162

AC:

AN:

278

Middle Eastern (MID)

AF:

0.110

AC:

178

AN:

1620

European-Non Finnish (NFE)

AF:

0.148

AC:

112824

AN:

761898

Other (OTH)

AF:

0.127

AC:

3478

AN:

27298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

6380

12760

19141

25521

31901

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5478

10956

16434

21912

27390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.131

AC:

19924

AN:

152162

Hom.:

1435

Cov.:

AF XY:

0.130

AC XY:

9635

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.111

AC:

4603

AN:

41528

American (AMR)

AF:

0.113

AC:

1735

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

546

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5172

South Asian (SAS)

AF:

0.0516

AC:

249

AN:

4822

European-Finnish (FIN)

AF:

0.193

AC:

2036

AN:

10574

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.152

AC:

10363

AN:

67982

Other (OTH)

AF:

0.128

AC:

271

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

873

1746

2619

3492

4365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.140

Hom.:

4561

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

(source)

DANN

Benign

0.54

PhyloP100

-0.065

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over