Genetic Variant ENST00000609307.2:n.1099+946G>A (chr7-7564968-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . 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:

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new If you want to explore the variant's impact on the transcript ENST00000609307.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609307.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIOS-DT	NR_110084.1		n.153-644G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
MIOS-DT	ENST00000609307.2	TSL:3	n.1099+946G>A	intron	N/A
MIOS-DT	ENST00000609497.6	TSL:2	n.1083+946G>A	intron	N/A
MIOS-DT	ENST00000729942.1		n.508+946G>A	intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over