chr5-137870267-T-A

Position:

• chr5-137870267-T-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_006790.3(MYOT):​c.-211-174T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 148,324 control chromosomes in the GnomAD database, including 168 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.027 (168 hom., cov: 29)
• Consequence: MYOT NM_006790.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.808

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 5-137870267-T-A is Benign according to our data. Variant chr5-137870267-T-A is described in ClinVar as [Benign]. Clinvar id is 1178361.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0883 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYOT	NM_006790.3	c.-211-174T>A		intron_variant		ENST00000239926.9	NP_006781.1
PKD2L2-DT	XR_948815.3	n.303-11004A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYOT	ENST00000239926.9	c.-211-174T>A		intron_variant		1	NM_006790.3	ENSP00000239926	P1
PKD2L2-DT	ENST00000514616.6	n.320-11004A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4033 AN: 148216 Hom.: 167 Cov.: 29

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.0771

Gnomad AMR AF: 0.0124

Gnomad ASJ AF: 0.00607

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000857

Gnomad FIN AF: 0.000102

Gnomad MID AF: 0.0230

Gnomad NFE AF: 0.00114

Gnomad OTH AF: 0.0188

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

GnomAD4 genome AF: 0.0272 AC: 4040 AN: 148324 Hom.: 168 Cov.: 29 AF XY: 0.0266 AC XY: 1915 AN XY: 72050

Gnomad4 AFR AF: 0.0907

Gnomad4 AMR AF: 0.0123

Gnomad4 ASJ AF: 0.00607

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000644

Gnomad4 FIN AF: 0.000102

Gnomad4 NFE AF: 0.00114

Gnomad4 OTH AF: 0.0191

Alfa AF: 0.0201 Hom.: 6

Bravo AF: 0.0308

Asia WGS AF: 0.00607 AC: 21 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 15, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.22

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: rs58860731; hg19: chr5-137205956;