dbSNP rs764551: ZFP1:c.*50C>A (chr16-75170384-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_153688.4(ZFP1):c.*50C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,507,764 control chromosomes in the GnomAD database, including 20,063 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 0.11 ( 1932 hom., cov: 32)

Exomes 𝑓: 0.13 ( 18131 hom. )

Consequence

ZFP1
NM_153688.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

Publications

12 publications found

Variant links:

Genes affected

ZFP1 (HGNC:23328): (ZFP1 zinc finger protein) This gene belongs to the zinc finger protein family. Some members of this family bind to DNA by zinc-mediated secondary structures called zinc fingers, and are involved in transcriptional regulation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

ZFP1 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFP1	NM_153688.4 link	c.*50C>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000570010.6	NP_710155.2	Q6P2D0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFP1	ENST00000570010.6 link	c.*50C>A		3_prime_UTR_variant	Exon 4 of 4	2	NM_153688.4	ENSP00000457044.1		Q6P2D0-1

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17327

AN:

151986

Hom.:

1931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0435

Gnomad AMI

AF:

0.0791

Gnomad AMR

AF:

0.137

Gnomad ASJ

AF:

0.0896

Gnomad EAS

AF:

0.618

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.0993

Gnomad OTH

AF:

0.108

GnomAD2 exomes

AF:

0.176

AC:

30606

AN:

174116

AF XY:

0.175

show subpopulations

Gnomad AFR exome

AF:

0.0425

Gnomad AMR exome

AF:

0.189

Gnomad ASJ exome

AF:

0.0911

Gnomad EAS exome

AF:

0.622

Gnomad FIN exome

AF:

0.142

Gnomad NFE exome

AF:

0.105

Gnomad OTH exome

AF:

0.155

GnomAD4 exome

AF:

0.129

AC:

174443

AN:

1355662

Hom.:

18131

Cov.:

AF XY:

0.132

AC XY:

87373

AN XY:

663196

show subpopulations

African (AFR)

AF:

0.0419

AC:

1263

AN:

30172

American (AMR)

AF:

0.178

AC:

5171

AN:

29084

Ashkenazi Jewish (ASJ)

AF:

0.0890

AC:

1764

AN:

19816

East Asian (EAS)

AF:

0.650

AC:

25206

AN:

38806

South Asian (SAS)

AF:

0.272

AC:

18227

AN:

67098

European-Finnish (FIN)

AF:

0.139

AC:

6795

AN:

49032

Middle Eastern (MID)

AF:

0.106

AC:

529

AN:

5010

European-Non Finnish (NFE)

AF:

0.102

AC:

107924

AN:

1060830

Other (OTH)

AF:

0.136

AC:

7564

AN:

55814

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

6436

12871

19307

25742

32178

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4490

8980

13470

17960

22450

<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:

0.114

AC:

17326

AN:

152102

Hom.:

1932

Cov.:

AF XY:

0.120

AC XY:

8952

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.0435

AC:

1806

AN:

41530

American (AMR)

AF:

0.137

AC:

2094

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.0896

AC:

311

AN:

3470

East Asian (EAS)

AF:

0.618

AC:

3187

AN:

5160

South Asian (SAS)

AF:

0.286

AC:

1380

AN:

4818

European-Finnish (FIN)

AF:

0.138

AC:

1456

AN:

10554

Middle Eastern (MID)

AF:

0.127

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0993

AC:

6755

AN:

67998

Other (OTH)

AF:

0.108

AC:

228

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

685

1370

2054

2739

3424

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.106

Hom.:

1164

Bravo

AF:

0.113

Asia WGS

AF:

0.406

AC:

1408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.10

(source)

DANN

Benign

0.53

PhyloP100

-1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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