Genetic Variant ENST00000703449.1:c.-171+3153A>G (chr16-3267036-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000703449.1(ZNF263):c.-171+3153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,168 control chromosomes in the GnomAD database, including 3,650 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 0.20 ( 3650 hom., cov: 32)

Exomes 𝑓: 0.38 ( 0 hom. )

Consequence

ZNF263
ENST00000703449.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.563

Publications

11 publications found

Variant links:

Genes affected

ZNF263 (HGNC:13056): (zinc finger protein 263) Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and transcription cis-regulatory region binding activity. Involved in negative regulation of transcription by RNA polymerase II and positive regulation of transcription by RNA polymerase II. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF263 links:

LINC00921 (HGNC:26830): (long intergenic non-protein coding RNA 921)

LINC00921 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=-0.93).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00921	NR_033904.1 link	n.2002-90A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ZNF263	ENST00000703449.1 link	c.-171+3153A>G	intron_variant	Intron 1 of 1		ENSP00000515300.1	B4DI05
LINC00921	ENST00000572123.4 link	n.188-90A>G	intron_variant	Intron 2 of 2	5
LINC00921	ENST00000573951.1 link	n.2027-90A>G	intron_variant	Intron 1 of 1	2
LINC00921	ENST00000706009.1 link	n.71-90A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.198

AC:

30160

AN:

152042

Hom.:

3651

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0792

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.0387

Gnomad SAS

AF:

0.126

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.210

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

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:

0.198

AC:

30157

AN:

152160

Hom.:

3650

Cov.:

AF XY:

0.201

AC XY:

14945

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0790

AC:

3279

AN:

41524

American (AMR)

AF:

0.292

AC:

4457

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

776

AN:

3470

East Asian (EAS)

AF:

0.0387

AC:

201

AN:

5188

South Asian (SAS)

AF:

0.126

AC:

609

AN:

4828

European-Finnish (FIN)

AF:

0.294

AC:

3109

AN:

10564

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.250

AC:

17011

AN:

67998

Other (OTH)

AF:

0.207

AC:

437

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1201

2401

3602

4802

6003

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

320

640

960

1280

1600

<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:

0.234

Hom.:

595

Bravo

AF:

0.196

Asia WGS

AF:

0.0880

AC:

310

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

1.8

(source)

DANN

Benign

0.62

PhyloP100

-0.56

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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