5-137870871-C-A

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2

The NM_006790.3(MYOT):​c.220C>A​(p.Gln74Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00253 in 1,614,194 control chromosomes in the GnomAD database, including 88 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.013 ( 44 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 44 hom. )

Consequence

MYOT
NM_006790.3 missense

Scores

5

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 3.80
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 -18 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.07220766).
BP6
Variant 5-137870871-C-A is Benign according to our data. Variant chr5-137870871-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 464369.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0134 (2048/152308) while in subpopulation AFR AF= 0.0463 (1926/41554). AF 95% confidence interval is 0.0446. There are 44 homozygotes in gnomad4. There are 965 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2048 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MYOTNM_006790.3 linkuse as main transcriptc.220C>A p.Gln74Lys missense_variant 2/10 ENST00000239926.9
PKD2L2-DTXR_948815.3 linkuse as main transcriptn.303-11608G>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MYOTENST00000239926.9 linkuse as main transcriptc.220C>A p.Gln74Lys missense_variant 2/101 NM_006790.3 P1
PKD2L2-DTENST00000514616.6 linkuse as main transcriptn.320-11608G>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0134
AC:
2040
AN:
152190
Hom.:
44
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0463
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00537
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.0119
GnomAD4 exome
AF:
0.00140
AC:
2040
AN:
1461886
Hom.:
44
Cov.:
31
AF XY:
0.00121
AC XY:
877
AN XY:
727246
show subpopulations
Gnomad4 AFR exome
AF:
0.0470
Gnomad4 AMR exome
AF:
0.00264
Gnomad4 ASJ exome
AF:
0.000918
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000104
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000134
Gnomad4 OTH exome
AF:
0.00253
GnomAD4 genome
AF:
0.0134
AC:
2048
AN:
152308
Hom.:
44
Cov.:
32
AF XY:
0.0130
AC XY:
965
AN XY:
74488
show subpopulations
Gnomad4 AFR
AF:
0.0463
Gnomad4 AMR
AF:
0.00536
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.0118
Alfa
AF:
0.00214
Hom.:
12
Bravo
AF:
0.0159

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:2
Benign, criteria provided, single submitterclinical testingMendelicsMay 04, 2022- -
Benign, criteria provided, single submitterclinical testingGeneDxNov 09, 2017This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsSep 28, 2017- -
Myofibrillar myopathy 3 Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_noAF
Benign
-0.58
CADD
Benign
19
LIST_S2
Benign
0.54
T
MetaRNN
Benign
0.072
T
Sift4G
Benign
0.94
T
Vest4
0.91
gMVP
0.48

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: rs6890689; hg19: chr5-137206560; API