dbSNP rs2279025: MYG1:c.490-199C>A (chr12-53305709-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_021640.4(MYG1):c.490-199C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000898 in 445,234 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000090 ( 0 hom. )

Consequence

MYG1
NM_021640.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.216

Publications

0 publications found

Variant links:

Genes affected

MYG1 (HGNC:17590): (MYG1 exonuclease) Predicted to enable nuclease activity. Predicted to be involved in nucleic acid phosphodiester bond hydrolysis. Predicted to act upstream of or within locomotory exploration behavior. Located in mitochondrion and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MYG1 links:

ENSG00000288663 (HGNC:):

ENSG00000288663 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYG1	NM_021640.4 link	c.490-199C>A		intron_variant	Intron 3 of 6	ENST00000267103.10	NP_067653.4	Q9HB07

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYG1	ENST00000267103.10 link	c.490-199C>A		intron_variant	Intron 3 of 6	1	NM_021640.4	ENSP00000267103.5		Q9HB07

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000898

AC:

AN:

445234

Hom.:

Cov.:

AF XY:

0.0000131

AC XY:

AN XY:

229358

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11740

American (AMR)

AF:

0.00

AC:

AN:

11980

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12268

East Asian (EAS)

AF:

0.00

AC:

AN:

26284

South Asian (SAS)

AF:

0.000117

AC:

AN:

34244

European-Finnish (FIN)

AF:

0.00

AC:

AN:

26386

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1864

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

296140

Other (OTH)

AF:

0.00

AC:

AN:

24328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

5.9

(source)

DANN

Benign

0.83

PhyloP100

0.22

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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