5-137870288-G-GACAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006790.3(MYOT):​c.-211-117_-211-114dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.16 ( 1843 hom., cov: 0)

Consequence

MYOT
NM_006790.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00
Variant links:
Genes affected
MYOT (HGNC:12399): (myotilin) This gene encodes a cystoskeletal protein which plays a significant role in the stability of thin filaments during muscle contraction. This protein binds F-actin, crosslinks actin filaments, and prevents latrunculin A-induced filament disassembly. Mutations in this gene have been associated with limb-girdle muscular dystrophy and myofibrillar myopathies. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined.[provided by RefSeq, Oct 2008]
PKD2L2-DT (HGNC:55557): (PKD2L2 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 5-137870288-G-GACAC is Benign according to our data. Variant chr5-137870288-G-GACAC is described in ClinVar as [Benign]. Clinvar id is 1225913.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYOTNM_006790.3 linkuse as main transcriptc.-211-117_-211-114dup intron_variant ENST00000239926.9
PKD2L2-DTXR_948815.3 linkuse as main transcriptn.303-11026_303-11025insGTGT intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYOTENST00000239926.9 linkuse as main transcriptc.-211-117_-211-114dup intron_variant 1 NM_006790.3 P1
PKD2L2-DTENST00000514616.6 linkuse as main transcriptn.320-11026_320-11025insGTGT intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.161
AC:
20468
AN:
126754
Hom.:
1838
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.152
Gnomad AMI
AF:
0.0727
Gnomad AMR
AF:
0.224
Gnomad ASJ
AF:
0.145
Gnomad EAS
AF:
0.315
Gnomad SAS
AF:
0.249
Gnomad FIN
AF:
0.128
Gnomad MID
AF:
0.152
Gnomad NFE
AF:
0.144
Gnomad OTH
AF:
0.158
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.161
AC:
20481
AN:
126828
Hom.:
1843
Cov.:
0
AF XY:
0.166
AC XY:
9980
AN XY:
60106
show subpopulations
Gnomad4 AFR
AF:
0.153
Gnomad4 AMR
AF:
0.224
Gnomad4 ASJ
AF:
0.145
Gnomad4 EAS
AF:
0.314
Gnomad4 SAS
AF:
0.250
Gnomad4 FIN
AF:
0.128
Gnomad4 NFE
AF:
0.144
Gnomad4 OTH
AF:
0.159

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 06, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs35301804; hg19: chr5-137205977; API