chr5-137870288-GACACACACACAC-G

Variant names:

• chr5-137870288-GACACACACACAC-G
• rs35301804
• NM_006790.3:c.-211-125_-211-114delCACACACACACA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_006790.3(MYOT):​c.-211-125_-211-114delCACACACACACA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0019 (3 hom., cov: 0)
• Consequence: MYOT NM_006790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

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)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00187 (238/127084) while in subpopulation SAS AF= 0.0231 (83/3590). AF 95% confidence interval is 0.0191. There are 3 homozygotes in gnomad4. There are 117 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 238 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYOT	NM_006790.3	c.-211-125_-211-114delCACACACACACA		intron_variant	Intron 1 of 9	ENST00000239926.9	NP_006781.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYOT	ENST00000239926.9	c.-211-152_-211-141delACACACACACAC		intron_variant	Intron 1 of 9	1	NM_006790.3	ENSP00000239926.4

Frequencies

GnomAD3 genomes AF: 0.00188 AC: 239 AN: 127010 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.000542

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00205

Gnomad ASJ AF: 0.00371

Gnomad EAS AF: 0.000227

Gnomad SAS AF: 0.0233

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0210

Gnomad NFE AF: 0.00138

Gnomad OTH AF: 0.00529

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

GnomAD4 genome AF: 0.00187 AC: 238 AN: 127084 Hom.: 3 Cov.: 0 AF XY: 0.00194 AC XY: 117 AN XY: 60226

Gnomad4 AFR AF: 0.000540

Gnomad4 AMR AF: 0.00205

Gnomad4 ASJ AF: 0.00371

Gnomad4 EAS AF: 0.000228

Gnomad4 SAS AF: 0.0231

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00138

Gnomad4 OTH AF: 0.00523

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35301804; hg19: chr5-137205977;