chr15-63043708-C-G
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The ENST00000267996.11(TPM1):c.117C>G(p.Leu39Leu) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00117 in 1,546,258 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000267996.11 splice_region, synonymous
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00108 AC: 164AN: 152180Hom.: 2 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00246 AC: 347AN: 141004 AF XY: 0.00304 show subpopulations
GnomAD4 exome AF: 0.00118 AC: 1641AN: 1393960Hom.: 21 Cov.: 31 AF XY: 0.00138 AC XY: 952AN XY: 687550 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00107 AC: 163AN: 152298Hom.: 2 Cov.: 32 AF XY: 0.00124 AC XY: 92AN XY: 74476 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:2
Leu39Leu in exon 1A of TPM1: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and has been identified in 1.2% (7/572) of Asian chromosomes from a broad population by the 1000 Genomes project (dbSNP rs201720832). -
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not provided Benign:2
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TPM1: BP4, BP7, BS1, BS2 -
Cardiomyopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at