dbSNP rs11204210: ZNF488:p.Gly21Gly (chr10-47368767-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_153034.4(ZNF488):c.63G>A(p.Gly21Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,611,982 control chromosomes in the GnomAD database, including 91,649 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 0.33 ( 8680 hom., cov: 33)

Exomes 𝑓: 0.33 ( 82969 hom. )

Consequence

ZNF488
NM_153034.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.349

Publications

9 publications found

Variant links:

Genes affected

ZNF488 (HGNC:23535): (zinc finger protein 488) Predicted to enable DNA binding activity and metal ion binding activity. Predicted to be involved in oligodendrocyte development; positive regulation of myelination; and regulation of transcription, DNA-templated. Predicted to act upstream of or within negative regulation of transcription, DNA-templated and positive regulation of oligodendrocyte differentiation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF488 links:

Genome browser will be placed here

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=-0.85).

BP7

Synonymous conserved (PhyloP=-0.349 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZNF488	NM_153034.4 link	c.63G>A	p.Gly21Gly	synonymous_variant	Exon 2 of 2	ENST00000585316.3	NP_694579.1	Q96MN9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF488	ENST00000585316.3 link	c.63G>A	p.Gly21Gly	synonymous_variant	Exon 2 of 2	1	NM_153034.4	ENSP00000462269.1		Q96MN9-1
ZNF488	ENST00000591025.1 link	c.-153G>A		5_prime_UTR_variant	Exon 2 of 3	1		ENSP00000468133.1		Q96MN9-2

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50873

AN:

152040

Hom.:

8668

Cov.:

show subpopulations

Gnomad AFR

AF:

0.344

Gnomad AMI

AF:

0.218

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.492

Gnomad SAS

AF:

0.439

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.326

Gnomad OTH

AF:

0.336

GnomAD2 exomes

AF:

0.344

AC:

85496

AN:

248178

AF XY:

0.352

show subpopulations

Gnomad AFR exome

AF:

0.345

Gnomad AMR exome

AF:

0.270

Gnomad ASJ exome

AF:

0.367

Gnomad EAS exome

AF:

0.504

Gnomad FIN exome

AF:

0.310

Gnomad NFE exome

AF:

0.321

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

AF:

0.334

AC:

487949

AN:

1459824

Hom.:

82969

Cov.:

AF XY:

0.338

AC XY:

245756

AN XY:

726196

show subpopulations

African (AFR)

AF:

0.344

AC:

11501

AN:

33454

American (AMR)

AF:

0.273

AC:

12172

AN:

44586

Ashkenazi Jewish (ASJ)

AF:

0.361

AC:

9408

AN:

26052

East Asian (EAS)

AF:

0.481

AC:

19090

AN:

39694

South Asian (SAS)

AF:

0.437

AC:

37603

AN:

86046

European-Finnish (FIN)

AF:

0.304

AC:

15959

AN:

52474

Middle Eastern (MID)

AF:

0.407

AC:

2340

AN:

5754

European-Non Finnish (NFE)

AF:

0.323

AC:

358658

AN:

1111436

Other (OTH)

AF:

0.352

AC:

21218

AN:

60328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

21083

42166

63250

84333

105416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11836

23672

35508

47344

59180

<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:

0.335

AC:

50920

AN:

152158

Hom.:

8680

Cov.:

AF XY:

0.336

AC XY:

24993

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.344

AC:

14293

AN:

41514

American (AMR)

AF:

0.289

AC:

4420

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

1206

AN:

3470

East Asian (EAS)

AF:

0.493

AC:

2546

AN:

5166

South Asian (SAS)

AF:

0.438

AC:

2111

AN:

4824

European-Finnish (FIN)

AF:

0.297

AC:

3143

AN:

10598

Middle Eastern (MID)

AF:

0.405

AC:

119

AN:

294

European-Non Finnish (NFE)

AF:

0.326

AC:

22166

AN:

67980

Other (OTH)

AF:

0.339

AC:

717

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1790

3580

5370

7160

8950

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.327

Hom.:

5569

Bravo

AF:

0.332

Asia WGS

AF:

0.462

AC:

1604

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.0

(source)

DANN

Benign

0.48

PhyloP100

-0.35

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