dbSNP rs10512421: ZNF286B:n.347-124C>T (chr17-18663351-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000285274.9(ZNF286B):n.347-124C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 1,497,356 control chromosomes in the GnomAD database, including 2,252 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 0.071 ( 1266 hom., cov: 32)

Exomes 𝑓: 0.0081 ( 986 hom. )

Consequence

ZNF286B
ENST00000285274.9 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.533

Publications

4 publications found

Variant links:

Genes affected

ZNF286B (HGNC:):

ZNF286B links:

ZNF286B (HGNC:33241): (zinc finger protein 286B (pseudogene)) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF286B 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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF286B	NR_160540.1 link	n.433-124C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF286B	ENST00000285274.9 link	n.347-124C>T		intron_variant	Intron 3 of 3	3
ZNF286B	ENST00000668878.2 link	n.322-124C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0707

AC:

10748

AN:

152054

Hom.:

1263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0275

Gnomad ASJ

AF:

0.0231

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.00173

Gnomad OTH

AF:

0.0522

GnomAD4 exome

AF:

0.00812

AC:

10921

AN:

1345184

Hom.:

986

AF XY:

0.00733

AC XY:

4835

AN XY:

659558

show subpopulations

African (AFR)

AF:

0.248

AC:

7419

AN:

29886

American (AMR)

AF:

0.0180

AC:

551

AN:

30682

Ashkenazi Jewish (ASJ)

AF:

0.0207

AC:

460

AN:

22170

East Asian (EAS)

AF:

0.000113

AC:

AN:

35382

South Asian (SAS)

AF:

0.000800

AC:

AN:

71294

European-Finnish (FIN)

AF:

0.0000240

AC:

AN:

41614

Middle Eastern (MID)

AF:

0.0211

AC:

115

AN:

5438

European-Non Finnish (NFE)

AF:

0.00105

AC:

1103

AN:

1052784

Other (OTH)

AF:

0.0217

AC:

1211

AN:

55934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

490

979

1469

1958

2448

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

256

512

768

1024

1280

<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:

0.0708

AC:

10770

AN:

152172

Hom.:

1266

Cov.:

AF XY:

0.0691

AC XY:

5143

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.242

AC:

10021

AN:

41480

American (AMR)

AF:

0.0274

AC:

419

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0231

AC:

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5184

South Asian (SAS)

AF:

0.00104

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10600

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00174

AC:

118

AN:

68004

Other (OTH)

AF:

0.0516

AC:

109

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

417

834

1251

1668

2085

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<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:

0.0244

Hom.:

709

Bravo

AF:

0.0796

Asia WGS

AF:

0.0180

AC:

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

8.4

(source)

DANN

Benign

0.43

PhyloP100

0.53

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