12-53300705-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000267103.10(MYG1):​c.329+443C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,150 control chromosomes in the GnomAD database, including 65,298 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 0.92 ( 65298 hom., cov: 30)

Consequence

MYG1
ENST00000267103.10 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYG1NM_021640.4 linkuse as main transcriptc.329+443C>T intron_variant ENST00000267103.10 NP_067653.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYG1ENST00000267103.10 linkuse as main transcriptc.329+443C>T intron_variant 1 NM_021640.4 ENSP00000267103 P1

Frequencies

GnomAD3 genomes
AF:
0.921
AC:
140055
AN:
152032
Hom.:
65265
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.765
Gnomad AMI
AF:
0.987
Gnomad AMR
AF:
0.969
Gnomad ASJ
AF:
0.991
Gnomad EAS
AF:
0.958
Gnomad SAS
AF:
0.916
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
0.965
Gnomad NFE
AF:
0.985
Gnomad OTH
AF:
0.953
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.921
AC:
140143
AN:
152150
Hom.:
65298
Cov.:
30
AF XY:
0.922
AC XY:
68616
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.765
Gnomad4 AMR
AF:
0.969
Gnomad4 ASJ
AF:
0.991
Gnomad4 EAS
AF:
0.958
Gnomad4 SAS
AF:
0.917
Gnomad4 FIN
AF:
1.00
Gnomad4 NFE
AF:
0.985
Gnomad4 OTH
AF:
0.953
Alfa
AF:
0.928
Hom.:
6483
Bravo
AF:
0.913
Asia WGS
AF:
0.920
AC:
3202
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
7.6
DANN
Benign
0.80

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4759054; hg19: chr12-53694489; API