Genetic Variant ZNF277-AS1:n.352-22549C>A (chr7-112350947-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000431064.1(ZNF277-AS1):n.352-22549C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,286 control chromosomes in the GnomAD database, including 346 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 0.044 ( 346 hom., cov: 32)

Consequence

ZNF277-AS1
ENST00000431064.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.800

Publications

0 publications found

Variant links:

Genes affected

ZNF277-AS1 (HGNC:55828): (ZNF277 antisense RNA 1)

ZNF277-AS1 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ZNF277-AS1	ENST00000431064.1 link	n.352-22549C>A	intron_variant	Intron 3 of 3	3
ZNF277-AS1	ENST00000847105.1 link	n.283-22549C>A	intron_variant	Intron 2 of 2
ZNF277-AS1	ENST00000847106.1 link	n.445-9825C>A	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.0437

AC:

6650

AN:

152168

Hom.:

344

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0223

Gnomad ASJ

AF:

0.0219

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0245

Gnomad FIN

AF:

0.00621

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0101

Gnomad OTH

AF:

0.0378

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0438

AC:

6674

AN:

152286

Hom.:

346

Cov.:

AF XY:

0.0420

AC XY:

3129

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.127

AC:

5294

AN:

41546

American (AMR)

AF:

0.0223

AC:

341

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0219

AC:

AN:

3472

East Asian (EAS)

AF:

0.00116

AC:

AN:

5188

South Asian (SAS)

AF:

0.0245

AC:

118

AN:

4818

European-Finnish (FIN)

AF:

0.00621

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0101

AC:

686

AN:

68014

Other (OTH)

AF:

0.0374

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

296

592

887

1183

1479

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

228

304

380

<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:

0.0285

Hom.:

Bravo

AF:

0.0484

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.9

(source)

DANN

Benign

0.53

PhyloP100

0.80

Mutation Taster

=100/0

polymorphism

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over