Genetic Variant ZNF75A:c.934+39G>A (chr16-3317061-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 NM_001302109.2(ZNF75A):c.934+39G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,575,034 control chromosomes in the GnomAD database, including 39,200 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 0.21 ( 3724 hom., cov: 32)

Exomes 𝑓: 0.22 ( 35476 hom. )

Consequence

ZNF75A
NM_001302109.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.355

Publications

20 publications found

Variant links:

Genes affected

ZNF75A (HGNC:13146): (zinc finger protein 75A) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF75A links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001302109.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF75A	NM_001302109.2	MANE Select	c.934+39G>A	intron	N/A	NP_001289038.1	A0A590UJE0
ZNF75A	NM_001324041.1		c.934+39G>A	intron	N/A	NP_001310970.1	A0A590UJE0
ZNF75A	NM_153028.4		c.211+39G>A	intron	N/A	NP_694573.1	Q96N20

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZNF75A	ENST00000669516.2	MANE Select	c.934+39G>A	intron	N/A	ENSP00000499415.1	A0A590UJE0
ZNF75A	ENST00000617839.1	TSL:1	c.211+39G>A	intron	N/A	ENSP00000482769.1	Q96N20
ZNF75A	ENST00000938990.1		c.907+39G>A	intron	N/A	ENSP00000609049.1

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32563

AN:

151930

Hom.:

3723

Cov.:

show subpopulations

Gnomad AFR

AF:

0.188

Gnomad AMI

AF:

0.213

Gnomad AMR

AF:

0.278

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.0372

Gnomad SAS

AF:

0.0977

Gnomad FIN

AF:

0.282

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.202

GnomAD2 exomes

AF:

0.221

AC:

51624

AN:

233216

AF XY:

0.213

show subpopulations

Gnomad AFR exome

AF:

0.183

Gnomad AMR exome

AF:

0.346

Gnomad ASJ exome

AF:

0.208

Gnomad EAS exome

AF:

0.0426

Gnomad FIN exome

AF:

0.289

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.224

GnomAD4 exome

AF:

0.217

AC:

308729

AN:

1422986

Hom.:

35476

Cov.:

AF XY:

0.213

AC XY:

150887

AN XY:

708650

show subpopulations

African (AFR)

AF:

0.179

AC:

5748

AN:

32180

American (AMR)

AF:

0.328

AC:

13222

AN:

40360

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

4992

AN:

25238

East Asian (EAS)

AF:

0.0380

AC:

1502

AN:

39522

South Asian (SAS)

AF:

0.106

AC:

8710

AN:

82184

European-Finnish (FIN)

AF:

0.281

AC:

14948

AN:

53214

Middle Eastern (MID)

AF:

0.112

AC:

630

AN:

5646

European-Non Finnish (NFE)

AF:

0.228

AC:

247294

AN:

1085666

Other (OTH)

AF:

0.198

AC:

11683

AN:

58976

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

11982

23965

35947

47930

59912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8228

16456

24684

32912

41140

<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:

0.214

AC:

32578

AN:

152048

Hom.:

3724

Cov.:

AF XY:

0.215

AC XY:

16015

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.188

AC:

7792

AN:

41500

American (AMR)

AF:

0.277

AC:

4234

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.192

AC:

665

AN:

3470

East Asian (EAS)

AF:

0.0373

AC:

193

AN:

5180

South Asian (SAS)

AF:

0.0976

AC:

470

AN:

4816

European-Finnish (FIN)

AF:

0.282

AC:

2973

AN:

10540

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.230

AC:

15607

AN:

67962

Other (OTH)

AF:

0.199

AC:

420

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1304

2607

3911

5214

6518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

336

672

1008

1344

1680

<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:

0.219

Hom.:

1638

Bravo

AF:

0.216

Asia WGS

AF:

0.0810

AC:

286

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.14

(source)

DANN

Benign

0.60

PhyloP100

-0.35

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over