Genetic Variant MYOSLID-AS1:n.260+9348G>A (chr2-207508272-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 ENST00000412387.5(MYOSLID-AS1):n.260+9348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,036 control chromosomes in the GnomAD database, including 9,159 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 0.31 ( 9159 hom., cov: 32)

Consequence

MYOSLID-AS1
ENST00000412387.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.271

Publications

17 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 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+9348G>A	intron_variant	Intron 3 of 4	4
MYOSLID-AS1	ENST00000418850.1 link	n.256+9348G>A	intron_variant	Intron 3 of 5	5
MYOSLID-AS1	ENST00000432413.3 link	n.242+9348G>A	intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47556

AN:

151918

Hom.:

9158

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0924

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.454

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.428

Gnomad OTH

AF:

0.288

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

GnomAD4 genome

AF:

0.313

AC:

47561

AN:

152036

Hom.:

9159

Cov.:

AF XY:

0.313

AC XY:

23269

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.0922

AC:

3827

AN:

41486

American (AMR)

AF:

0.359

AC:

5484

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1020

AN:

3470

East Asian (EAS)

AF:

0.128

AC:

661

AN:

5164

South Asian (SAS)

AF:

0.353

AC:

1695

AN:

4800

European-Finnish (FIN)

AF:

0.454

AC:

4791

AN:

10552

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.428

AC:

29085

AN:

67970

Other (OTH)

AF:

0.287

AC:

606

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1524

3048

4571

6095

7619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.375

Hom.:

33414

Bravo

AF:

0.297

Asia WGS

AF:

0.233

AC:

815

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

2.3

(source)

DANN

Benign

0.82

PhyloP100

-0.27

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