rs3215700
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_003289.4(TPM2):c.564-19del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000269 in 1,597,284 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000073 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000022 ( 0 hom. )
Consequence
TPM2
NM_003289.4 intron
NM_003289.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.39
Genes affected
TPM2 (HGNC:12011): (tropomyosin 2) This gene encodes beta-tropomyosin, a member of the actin filament binding protein family, and mainly expressed in slow, type 1 muscle fibers. Mutations in this gene can alter the expression of other sarcomeric tropomyosin proteins, and cause cap disease, nemaline myopathy and distal arthrogryposis syndromes. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 9-35684825-CG-C is Benign according to our data. Variant chr9-35684825-CG-C is described in ClinVar as [Benign]. Clinvar id is 1599464.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-35684825-CG-C is described in Lovd as [Benign].
BS2
?
High AC in GnomAd4 at 11 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TPM2 | NM_003289.4 | c.564-19del | intron_variant | ENST00000645482.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TPM2 | ENST00000645482.3 | c.564-19del | intron_variant | NM_003289.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000731 AC: 11AN: 150536Hom.: 0 Cov.: 0
GnomAD3 genomes
?
AF:
AC:
11
AN:
150536
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000221 AC: 32AN: 1446748Hom.: 0 Cov.: 36 AF XY: 0.0000195 AC XY: 14AN XY: 719592
GnomAD4 exome
AF:
AC:
32
AN:
1446748
Hom.:
Cov.:
36
AF XY:
AC XY:
14
AN XY:
719592
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0000731 AC: 11AN: 150536Hom.: 0 Cov.: 0 AF XY: 0.000123 AC XY: 9AN XY: 73382
GnomAD4 genome
?
AF:
AC:
11
AN:
150536
Hom.:
Cov.:
0
AF XY:
AC XY:
9
AN XY:
73382
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Arthrogryposis, distal, type 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at