dbSNP rs72954151: MYOSLID-AS1:n.260+27014T>C (chr2-207490606-A-G) – 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+27014T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 146,340 control chromosomes in the GnomAD database, including 13,116 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 0.37 ( 13116 hom., cov: 28)

Consequence

MYOSLID-AS1
ENST00000412387.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.595

Publications

1 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) 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+27014T>C	intron_variant	Intron 3 of 4	4
MYOSLID-AS1	ENST00000418850.1 link	n.256+27014T>C	intron_variant	Intron 3 of 5	5
MYOSLID-AS1	ENST00000432413.3 link	n.242+27014T>C	intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

53600

AN:

146218

Hom.:

13098

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.357

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.278

Gnomad SAS

AF:

0.386

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.319

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.345

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

GnomAD4 genome

AF:

0.367

AC:

53668

AN:

146340

Hom.:

13116

Cov.:

AF XY:

0.371

AC XY:

26456

AN XY:

71398

show subpopulations

African (AFR)

AF:

0.383

AC:

15675

AN:

40932

American (AMR)

AF:

0.433

AC:

6312

AN:

14582

Ashkenazi Jewish (ASJ)

AF:

0.333

AC:

1090

AN:

3270

East Asian (EAS)

AF:

0.278

AC:

1440

AN:

5174

South Asian (SAS)

AF:

0.385

AC:

1820

AN:

4724

European-Finnish (FIN)

AF:

0.375

AC:

3753

AN:

10016

Middle Eastern (MID)

AF:

0.321

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.348

AC:

22482

AN:

64526

Other (OTH)

AF:

0.354

AC:

710

AN:

2008

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1405

2810

4216

5621

7026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

484

968

1452

1936

2420

<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:

0.363

Hom.:

1486

Asia WGS

AF:

0.372

AC:

1293

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.6

(source)

DANN

Benign

0.73

PhyloP100

-0.59

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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