Genetic Variant MIOS-DT:n.1099+946G>A (chr7-7564968-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 ENST00000609307.2(MIOS-DT):n.1099+946G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 151,942 control chromosomes in the GnomAD database, including 171 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 0.031 ( 171 hom., cov: 32)

Consequence

MIOS-DT
ENST00000609307.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0570

Publications

2 publications found

Variant links:

Genes affected

MIOS-DT (HGNC:55187): (MIOS divergent transcript)

MIOS-DT 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIOS-DT	NR_110084.1 link	n.153-644G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIOS-DT	ENST00000609307.2 link	n.1099+946G>A	intron_variant	Intron 1 of 4	3
MIOS-DT	ENST00000609497.6 link	n.1083+946G>A	intron_variant	Intron 1 of 3	2
MIOS-DT	ENST00000729942.1 link	n.508+946G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0306

AC:

4652

AN:

151824

Hom.:

173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0846

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0212

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.0137

Gnomad SAS

AF:

0.00936

Gnomad FIN

AF:

0.00284

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00925

Gnomad OTH

AF:

0.0278

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

GnomAD4 genome

AF:

0.0306

AC:

4655

AN:

151942

Hom.:

171

Cov.:

AF XY:

0.0300

AC XY:

2227

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.0845

AC:

3495

AN:

41384

American (AMR)

AF:

0.0212

AC:

324

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3468

East Asian (EAS)

AF:

0.0139

AC:

AN:

5166

South Asian (SAS)

AF:

0.00895

AC:

AN:

4806

European-Finnish (FIN)

AF:

0.00284

AC:

AN:

10548

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00925

AC:

629

AN:

67980

Other (OTH)

AF:

0.0270

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

225

451

676

902

1127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0209

Hom.:

Bravo

AF:

0.0341

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.5

(source)

DANN

Benign

0.45

PhyloP100

-0.057

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