Genetic Variant MYOSLID-AS1:n.260+24506A>G (chr2-207493114-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 ENST00000412387.5(MYOSLID-AS1):n.260+24506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 146,784 control chromosomes in the GnomAD database, including 57,612 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 0.87 ( 57612 hom., cov: 29)

Consequence

MYOSLID-AS1
ENST00000412387.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.94

Publications

4 publications found

Variant links:

Genes affected

MYOSLID-AS1 (HGNC:):

MYOSLID-AS1 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
MYOSLID-AS1	ENST00000412387.5 link	n.260+24506A>G	intron_variant	Intron 3 of 4	4
MYOSLID-AS1	ENST00000418850.1 link	n.256+24506A>G	intron_variant	Intron 3 of 5	5
MYOSLID-AS1	ENST00000432413.3 link	n.242+24506A>G	intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.873

AC:

128023

AN:

146664

Hom.:

57565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.834

Gnomad AMI

AF:

0.927

Gnomad AMR

AF:

0.865

Gnomad ASJ

AF:

0.951

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.911

Gnomad FIN

AF:

0.912

Gnomad MID

AF:

0.894

Gnomad NFE

AF:

0.875

Gnomad OTH

AF:

0.899

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

GnomAD4 genome

AF:

0.873

AC:

128129

AN:

146784

Hom.:

57612

Cov.:

AF XY:

0.877

AC XY:

62761

AN XY:

71552

show subpopulations

African (AFR)

AF:

0.834

AC:

34253

AN:

41050

American (AMR)

AF:

0.864

AC:

12503

AN:

14464

Ashkenazi Jewish (ASJ)

AF:

0.951

AC:

3136

AN:

3296

East Asian (EAS)

AF:

0.999

AC:

5188

AN:

5192

South Asian (SAS)

AF:

0.911

AC:

4310

AN:

4730

European-Finnish (FIN)

AF:

0.912

AC:

9164

AN:

10050

Middle Eastern (MID)

AF:

0.889

AC:

249

AN:

280

European-Non Finnish (NFE)

AF:

0.875

AC:

56729

AN:

64862

Other (OTH)

AF:

0.900

AC:

1805

AN:

2006

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

670

1339

2009

2678

3348

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:

0.874

Hom.:

44510

Asia WGS

AF:

0.944

AC:

3275

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.36

(source)

DANN

Benign

0.36

PhyloP100

-1.9

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