dbSNP rs2275294: ZNF512B:c.1969-113C>T (chr20-63962894-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020713.3(ZNF512B):c.1969-113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 1,295,078 control chromosomes in the GnomAD database, including 48,966 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5614 hom., cov: 34)

Exomes 𝑓: 0.26 ( 43352 hom. )

Consequence

ZNF512B
NM_020713.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.200

Publications

16 publications found

Variant links:

Genes affected

ZNF512B (HGNC:29212): (zinc finger protein 512B) Predicted to enable DNA binding activity and metal ion binding activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF512B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 20-63962894-G-A is Benign according to our data. Variant chr20-63962894-G-A is described in ClinVar as Benign. ClinVar VariationId is 1234322.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF512B	NM_020713.3 link	c.1969-113C>T		intron_variant	Intron 12 of 16	ENST00000369888.6	NP_065764.1	Q96KM6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF512B	ENST00000369888.6 link	c.1969-113C>T		intron_variant	Intron 12 of 16	1	NM_020713.3	ENSP00000358904.1		Q96KM6

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38538

AN:

152032

Hom.:

5609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.383

Gnomad ASJ

AF:

0.395

Gnomad EAS

AF:

0.511

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.279

GnomAD4 exome

AF:

0.265

AC:

302780

AN:

1142928

Hom.:

43352

AF XY:

0.266

AC XY:

148791

AN XY:

559624

show subpopulations

African (AFR)

AF:

0.139

AC:

3597

AN:

25830

American (AMR)

AF:

0.445

AC:

9749

AN:

21932

Ashkenazi Jewish (ASJ)

AF:

0.393

AC:

7214

AN:

18342

East Asian (EAS)

AF:

0.533

AC:

18251

AN:

34218

South Asian (SAS)

AF:

0.304

AC:

18807

AN:

61842

European-Finnish (FIN)

AF:

0.265

AC:

8179

AN:

30854

Middle Eastern (MID)

AF:

0.261

AC:

960

AN:

3678

European-Non Finnish (NFE)

AF:

0.248

AC:

222646

AN:

897516

Other (OTH)

AF:

0.275

AC:

13377

AN:

48716

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

11842

23684

35525

47367

59209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7648

15296

22944

30592

38240

<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:

0.253

AC:

38557

AN:

152150

Hom.:

5614

Cov.:

AF XY:

0.257

AC XY:

19117

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.147

AC:

6127

AN:

41540

American (AMR)

AF:

0.383

AC:

5858

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.395

AC:

1372

AN:

3470

East Asian (EAS)

AF:

0.511

AC:

2627

AN:

5144

South Asian (SAS)

AF:

0.326

AC:

1577

AN:

4832

European-Finnish (FIN)

AF:

0.255

AC:

2695

AN:

10588

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.258

AC:

17503

AN:

67970

Other (OTH)

AF:

0.281

AC:

592

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1438

2876

4314

5752

7190

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.256

Hom.:

1579

Bravo

AF:

0.259

Asia WGS

AF:

0.394

AC:

1367

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jun 19, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 21665992) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.3

(source)

DANN

Benign

0.90

PhyloP100

0.20

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over