Genetic Variant NM_032434.4:c.*273T>G (chr2-27621734-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_032434.4(ZNF512):c.*273T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 335,862 control chromosomes in the GnomAD database, including 8,716 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 ( 3418 hom., cov: 32)

Exomes 𝑓: 0.24 ( 5298 hom. )

Consequence

ZNF512
NM_032434.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.85

Publications

27 publications found

Variant links:

Genes affected

ZNF512 (HGNC:29380): (zinc finger protein 512) This gene encodes a protein containing four putative zinc finger motifs. Zinc finger motifs may bind to proteins or nucleic acids. Zinc finger-containing proteins are involved in a variety of processes, including regulation of transcription. Alternative splicing results in multiple transcript variants for this gene. [provided by RefSeq, Sep 2012]

ZNF512 links:

ENSG00000259080 (HGNC:):

ENSG00000259080 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=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032434.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF512	NM_032434.4	MANE Select	c.*273T>G	3_prime_UTR	Exon 14 of 14	NP_115810.2
ZNF512	NM_001271286.2		c.*273T>G	3_prime_UTR	Exon 13 of 13	NP_001258215.1
ZNF512	NM_001271287.2		c.*273T>G	3_prime_UTR	Exon 13 of 13	NP_001258216.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ZNF512	ENST00000355467.6	TSL:2 MANE Select	c.*273T>G	3_prime_UTR	Exon 14 of 14	ENSP00000347648.3
ZNF512	ENST00000556601.5	TSL:1	c.*273T>G	3_prime_UTR	Exon 13 of 13	ENSP00000451572.2
ZNF512	ENST00000488055.1	TSL:2	n.1103T>G	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

31174

AN:

151942

Hom.:

3412

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.198

GnomAD4 exome

AF:

0.239

AC:

43990

AN:

183800

Hom.:

5298

Cov.:

AF XY:

0.245

AC XY:

23672

AN XY:

96478

show subpopulations

African (AFR)

AF:

0.194

AC:

1243

AN:

6412

American (AMR)

AF:

0.148

AC:

958

AN:

6454

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

1205

AN:

5730

East Asian (EAS)

AF:

0.331

AC:

3914

AN:

11840

South Asian (SAS)

AF:

0.329

AC:

7085

AN:

21532

European-Finnish (FIN)

AF:

0.233

AC:

1867

AN:

8030

Middle Eastern (MID)

AF:

0.168

AC:

126

AN:

748

European-Non Finnish (NFE)

AF:

0.224

AC:

25165

AN:

112578

Other (OTH)

AF:

0.232

AC:

2427

AN:

10476

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1595

3189

4784

6378

7973

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

236

472

708

944

1180

<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:

0.205

AC:

31215

AN:

152062

Hom.:

3418

Cov.:

AF XY:

0.206

AC XY:

15311

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.182

AC:

7532

AN:

41488

American (AMR)

AF:

0.154

AC:

2360

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

703

AN:

3472

East Asian (EAS)

AF:

0.348

AC:

1795

AN:

5154

South Asian (SAS)

AF:

0.310

AC:

1493

AN:

4820

European-Finnish (FIN)

AF:

0.214

AC:

2262

AN:

10572

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.210

AC:

14261

AN:

67962

Other (OTH)

AF:

0.199

AC:

420

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1261

2522

3783

5044

6305

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

344

688

1032

1376

1720

<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:

0.207

Hom.:

14731

Bravo

AF:

0.200

Asia WGS

AF:

0.339

AC:

1176

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

2.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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