Genetic Variant ZNF83:c.-322+1116G>A (chr19-52637196-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000301096.8(ZNF83):c.-322+1116G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,476 control chromosomes in the GnomAD database, including 320 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 0.063 ( 318 hom., cov: 31)

Exomes 𝑓: 0.072 ( 2 hom. )

Consequence

ZNF83
ENST00000301096.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.643

Publications

2 publications found

Variant links:

Genes affected

ZNF83 (HGNC:13158): (zinc finger protein 83) 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 located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF83 links:

LOC124904757 (HGNC:):

LOC124904757 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
LOC124904757		n.52637196C>T	intragenic_variant
ZNF83	NM_001105549.2 link	c.-663+1116G>A	intron_variant	Intron 1 of 5	NP_001099019.1	P51522-1A0A024R4L3
ZNF83	NM_001105550.2 link	c.-547+1116G>A	intron_variant	Intron 1 of 4	NP_001099020.1	P51522-1A0A024R4L3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF83	ENST00000301096.8 link	c.-322+1116G>A		intron_variant	Intron 1 of 2	3		ENSP00000301096.3		P51522-1

Frequencies

GnomAD3 genomes

AF:

0.0625

AC:

9494

AN:

151998

Hom.:

315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0695

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0578

Gnomad ASJ

AF:

0.0352

Gnomad EAS

AF:

0.0403

Gnomad SAS

AF:

0.0541

Gnomad FIN

AF:

0.0583

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0640

Gnomad OTH

AF:

0.0746

GnomAD4 exome

AF:

0.0722

AC:

AN:

360

Hom.:

AF XY:

0.0714

AC XY:

AN XY:

252

show subpopulations

African (AFR)

AF:

0.200

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.125

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0455

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0756

AC:

AN:

238

Other (OTH)

AF:

0.0313

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0625

AC:

9509

AN:

152116

Hom.:

318

Cov.:

AF XY:

0.0630

AC XY:

4686

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.0694

AC:

2878

AN:

41490

American (AMR)

AF:

0.0579

AC:

885

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0352

AC:

122

AN:

3468

East Asian (EAS)

AF:

0.0402

AC:

208

AN:

5168

South Asian (SAS)

AF:

0.0548

AC:

264

AN:

4816

European-Finnish (FIN)

AF:

0.0583

AC:

617

AN:

10586

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0640

AC:

4351

AN:

67986

Other (OTH)

AF:

0.0777

AC:

164

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

445

891

1336

1782

2227

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

216

324

432

540

<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:

0.0643

Hom.:

517

Bravo

AF:

0.0638

Asia WGS

AF:

0.0590

AC:

204

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.5

(source)

DANN

Benign

0.56

PhyloP100

-0.64

PromoterAI

0.0048

Neutral

(source)

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