Genetic Variant ENST00000840167.1:n.790+906G>A (chr22-26646142-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 ENST00000840167.1(ENSG00000309298):n.790+906G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,128 control chromosomes in the GnomAD database, including 2,176 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 0.16 ( 2176 hom., cov: 32)

Consequence

ENSG00000309298
ENST00000840167.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0570

Publications

13 publications found

Variant links:

Genes affected

ENSG00000309298 (HGNC:):

ENSG00000309298 links:

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000309298	ENST00000840167.1 link	n.790+906G>A	intron_variant	Intron 1 of 1
ENSG00000309298	ENST00000840168.1 link	n.214+131G>A	intron_variant	Intron 1 of 1
MIATNB	ENST00000717180.1 link	n.-221C>T	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.163

AC:

24812

AN:

152010

Hom.:

2171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.130

Gnomad AMI

AF:

0.224

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.146

Gnomad EAS

AF:

0.264

Gnomad SAS

AF:

0.308

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.184

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

GnomAD4 genome

AF:

0.163

AC:

24846

AN:

152128

Hom.:

2176

Cov.:

AF XY:

0.164

AC XY:

12230

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.130

AC:

5374

AN:

41492

American (AMR)

AF:

0.175

AC:

2673

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.146

AC:

506

AN:

3470

East Asian (EAS)

AF:

0.264

AC:

1362

AN:

5164

South Asian (SAS)

AF:

0.309

AC:

1485

AN:

4810

European-Finnish (FIN)

AF:

0.133

AC:

1411

AN:

10588

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.167

AC:

11355

AN:

68004

Other (OTH)

AF:

0.192

AC:

405

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1074

2147

3221

4294

5368

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.173

Hom.:

6890

Bravo

AF:

0.165

Asia WGS

AF:

0.318

AC:

1106

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.4

(source)

DANN

Benign

0.24

PhyloP100

0.057

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