chr5-137870288-GAC-G

Variant names:

• chr5-137870288-GAC-G
• rs35301804
• NM_006790.3:c.-211-115_-211-114delCA

Variant summary

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

The NM_006790.3(MYOT):​c.-211-115_-211-114delCA 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 0.011 (11 hom., cov: 0)
• Consequence: MYOT NM_006790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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 eas. gnomad4 allele frequency = 0.0113 (1431/127052) while in subpopulation EAS AF= 0.0196 (86/4392). AF 95% confidence interval is 0.0162. There are 11 homozygotes in gnomad4. There are 645 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1431 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYOT	NM_006790.3	c.-211-115_-211-114delCA		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_-211-151delAC		intron_variant	Intron 1 of 9	1	NM_006790.3	ENSP00000239926.4

Frequencies

GnomAD3 genomes AF: 0.0112 AC: 1423 AN: 126978 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.0346

Gnomad AMR AF: 0.0101

Gnomad ASJ AF: 0.00618

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.0119

Gnomad FIN AF: 0.00520

Gnomad MID AF: 0.0140

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0113 AC: 1431 AN: 127052 Hom.: 11 Cov.: 0 AF XY: 0.0107 AC XY: 645 AN XY: 60210

Gnomad4 AFR AF: 0.0106

Gnomad4 AMR AF: 0.0101

Gnomad4 ASJ AF: 0.00618

Gnomad4 EAS AF: 0.0196

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.00520

Gnomad4 NFE AF: 0.0117

Gnomad4 OTH AF: 0.0151

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs35301804; hg19: chr5-137205977;