Genetic Variant NM_001305203.2:c.1317A>G (chr16-68564104-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001305203.2(ZFP90):c.1317A>G(p.Gln439Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 1,613,866 control chromosomes in the GnomAD database, including 292,441 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 0.51 ( 22087 hom., cov: 32)

Exomes 𝑓: 0.60 ( 270354 hom. )

Consequence

ZFP90
NM_001305203.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0290

Publications

28 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP7

Synonymous conserved (PhyloP=-0.029 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFP90	NM_001305203.2 link	c.1317A>G	p.Gln439Gln	synonymous_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.1317A>G	p.Gln439Gln	synonymous_variant	Exon 5 of 5	1	NM_001305203.2	ENSP00000454418.2		Q8TF47-1

Frequencies

GnomAD3 genomes

AF:

0.514

AC:

78083

AN:

151924

Hom.:

22077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.714

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.562

Gnomad EAS

AF:

0.760

Gnomad SAS

AF:

0.659

Gnomad FIN

AF:

0.645

Gnomad MID

AF:

0.560

Gnomad NFE

AF:

0.607

Gnomad OTH

AF:

0.528

GnomAD2 exomes

AF:

0.603

AC:

150515

AN:

249410

AF XY:

0.610

show subpopulations

Gnomad AFR exome

AF:

0.250

Gnomad AMR exome

AF:

0.607

Gnomad ASJ exome

AF:

0.577

Gnomad EAS exome

AF:

0.757

Gnomad FIN exome

AF:

0.631

Gnomad NFE exome

AF:

0.605

Gnomad OTH exome

AF:

0.602

GnomAD4 exome

AF:

0.604

AC:

883640

AN:

1461824

Hom.:

270354

Cov.:

AF XY:

0.607

AC XY:

441479

AN XY:

727216

show subpopulations

African (AFR)

AF:

0.240

AC:

8038

AN:

33476

American (AMR)

AF:

0.599

AC:

26792

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.576

AC:

15052

AN:

26132

East Asian (EAS)

AF:

0.749

AC:

29726

AN:

39698

South Asian (SAS)

AF:

0.671

AC:

57876

AN:

86254

European-Finnish (FIN)

AF:

0.630

AC:

33649

AN:

53398

Middle Eastern (MID)

AF:

0.591

AC:

3411

AN:

5768

European-Non Finnish (NFE)

AF:

0.606

AC:

673393

AN:

1111988

Other (OTH)

AF:

0.591

AC:

35703

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

23759

47518

71277

95036

118795

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18210

36420

54630

72840

91050

<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:

0.514

AC:

78102

AN:

152042

Hom.:

22087

Cov.:

AF XY:

0.520

AC XY:

38659

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.255

AC:

10581

AN:

41472

American (AMR)

AF:

0.553

AC:

8461

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.562

AC:

1950

AN:

3470

East Asian (EAS)

AF:

0.762

AC:

3927

AN:

5156

South Asian (SAS)

AF:

0.660

AC:

3181

AN:

4822

European-Finnish (FIN)

AF:

0.645

AC:

6821

AN:

10572

Middle Eastern (MID)

AF:

0.544

AC:

160

AN:

294

European-Non Finnish (NFE)

AF:

0.607

AC:

41252

AN:

67936

Other (OTH)

AF:

0.529

AC:

1118

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1787

3574

5361

7148

8935

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

688

1376

2064

2752

3440

<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:

0.565

Hom.:

38806

Bravo

AF:

0.497

Asia WGS

AF:

0.601

AC:

2090

AN:

3478

EpiCase

AF:

0.590

EpiControl

AF:

0.590

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

6.9

(source)

DANN

Benign

0.71

PhyloP100

-0.029

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