dbSNP rs136544: MIATNB:n.1375+3289T>C (chr22-26855404-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000450963.6(MIATNB):n.1375+3289T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,058 control chromosomes in the GnomAD database, including 41,850 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 0.74 ( 41850 hom., cov: 31)

Consequence

MIATNB
ENST00000450963.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.189

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 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.1375+3289T>C	intron_variant	Intron 10 of 13	5
MIATNB	ENST00000716994.1 link	n.886+3300T>C	intron_variant	Intron 6 of 8
MIATNB	ENST00000716995.1 link	n.705-6578T>C	intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes

AF:

0.739

AC:

112312

AN:

151940

Hom.:

41803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.805

Gnomad AMI

AF:

0.726

Gnomad AMR

AF:

0.759

Gnomad ASJ

AF:

0.726

Gnomad EAS

AF:

0.680

Gnomad SAS

AF:

0.739

Gnomad FIN

AF:

0.714

Gnomad MID

AF:

0.712

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.729

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

GnomAD4 genome

AF:

0.739

AC:

112416

AN:

152058

Hom.:

41850

Cov.:

AF XY:

0.739

AC XY:

54964

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.805

AC:

33410

AN:

41478

American (AMR)

AF:

0.758

AC:

11586

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.726

AC:

2520

AN:

3470

East Asian (EAS)

AF:

0.680

AC:

3518

AN:

5176

South Asian (SAS)

AF:

0.741

AC:

3568

AN:

4814

European-Finnish (FIN)

AF:

0.714

AC:

7544

AN:

10568

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.704

AC:

47863

AN:

67958

Other (OTH)

AF:

0.729

AC:

1541

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1484

2969

4453

5938

7422

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

846

1692

2538

3384

4230

<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:

0.721

Hom.:

6921

Bravo

AF:

0.742

Asia WGS

AF:

0.713

AC:

2475

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.61

PhyloP100

0.19

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