Genetic Variant ZMIZ1-AS1:n.269-27708G>A (chr10-78862599-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 ENST00000838110.1(ZMIZ1-AS1):n.269-27708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,174 control chromosomes in the GnomAD database, including 18,208 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 0.43 ( 18208 hom., cov: 33)

Consequence

ZMIZ1-AS1
ENST00000838110.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.422

Publications

3 publications found

Variant links:

Genes affected

ZMIZ1-AS1 (HGNC:27433): (ZMIZ1 antisense RNA 1)

ZMIZ1-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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ZMIZ1-AS1	ENST00000838110.1 link	n.269-27708G>A	intron_variant	Intron 4 of 4
ZMIZ1-AS1	ENST00000838111.1 link	n.421-27708G>A	intron_variant	Intron 5 of 5
ZMIZ1-AS1	ENST00000838112.1 link	n.334+8715G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64846

AN:

152056

Hom.:

18148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.782

Gnomad AMI

AF:

0.173

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.646

Gnomad SAS

AF:

0.551

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.369

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

GnomAD4 genome

AF:

0.427

AC:

64968

AN:

152174

Hom.:

18208

Cov.:

AF XY:

0.429

AC XY:

31900

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.782

AC:

32503

AN:

41544

American (AMR)

AF:

0.332

AC:

5071

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.302

AC:

1048

AN:

3470

East Asian (EAS)

AF:

0.647

AC:

3353

AN:

5182

South Asian (SAS)

AF:

0.549

AC:

2647

AN:

4818

European-Finnish (FIN)

AF:

0.276

AC:

2916

AN:

10576

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.241

AC:

16379

AN:

67982

Other (OTH)

AF:

0.374

AC:

791

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1528

3056

4583

6111

7639

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

558

1116

1674

2232

2790

<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:

0.302

Hom.:

13888

Bravo

AF:

0.443

Asia WGS

AF:

0.595

AC:

2066

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

0.70

PhyloP100

-0.42

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