Genetic Variant ENST00000450963.6:n.1168+24020A>G (chr22-26814728-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000450963.6(MIATNB):n.1168+24020A>G variant causes a intron change. The variant allele was found at a frequency of 0.728 in 152,136 control chromosomes in the GnomAD database, including 40,658 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 0.73 ( 40658 hom., cov: 33)

Consequence

MIATNB
ENST00000450963.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.80

Publications

3 publications found

Variant links:

Genes affected

MIATNB (HGNC:50731): (MIAT neighbor)

MIATNB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.24).

BA1

GnomAd4 highest subpopulation (NFE) 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	TSL
MIATNB	ENST00000450963.6 link	n.1168+24020A>G	intron_variant	Intron 9 of 13	5
MIATNB	ENST00000716994.1 link	n.690+36143A>G	intron_variant	Intron 5 of 8
MIATNB	ENST00000716995.1 link	n.704+24020A>G	intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.728

AC:

110704

AN:

152018

Hom.:

40625

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.758

Gnomad AMR

AF:

0.720

Gnomad ASJ

AF:

0.826

Gnomad EAS

AF:

0.612

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.699

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.753

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

GnomAD4 genome

AF:

0.728

AC:

110785

AN:

152136

Hom.:

40658

Cov.:

AF XY:

0.722

AC XY:

53688

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.671

AC:

27830

AN:

41488

American (AMR)

AF:

0.720

AC:

11003

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.826

AC:

2866

AN:

3470

East Asian (EAS)

AF:

0.613

AC:

3173

AN:

5178

South Asian (SAS)

AF:

0.610

AC:

2942

AN:

4826

European-Finnish (FIN)

AF:

0.699

AC:

7394

AN:

10576

Middle Eastern (MID)

AF:

0.718

AC:

211

AN:

294

European-Non Finnish (NFE)

AF:

0.781

AC:

53085

AN:

67990

Other (OTH)

AF:

0.754

AC:

1590

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

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

842

1684

2526

3368

4210

<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:

0.761

Hom.:

82551

Bravo

AF:

0.725

Asia WGS

AF:

0.619

AC:

2150

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.24

CADD

Benign

(source)

DANN

Benign

0.73

PhyloP100

3.8

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