2-219418432-T-TGCGCCCGCCAGCC
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001927.4(DES):c.-30_-18dupGCGCCCGCCAGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00323 in 1,552,212 control chromosomes in the GnomAD database, including 173 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001927.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0182 AC: 2771AN: 152006Hom.: 99 Cov.: 32
GnomAD4 exome AF: 0.00160 AC: 2237AN: 1400096Hom.: 72 Cov.: 29 AF XY: 0.00134 AC XY: 930AN XY: 694576
GnomAD4 genome AF: 0.0183 AC: 2779AN: 152116Hom.: 101 Cov.: 32 AF XY: 0.0176 AC XY: 1309AN XY: 74382
ClinVar
Submissions by phenotype
not specified Benign:3
The variant is found in DCM,DCM-CRDM panel(s). -
Variant summary: DES c.-30_-18dup13 is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.0011 in 165222 control chromosomes, predominantly at a frequency of 0.024 within the African or African-American subpopulation in the gnomAD database, including 5 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 768-fold of the estimated maximal expected allele frequency for a pathogenic variant in DES causing Dilated Cardiomyopathy phenotype (3.1e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. A co-occurrence with a pathogenic variant has been reported (MYBPC3 c.3330+5G>C; Internal testing), providing supporting evidence for a benign role. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign. -
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not provided Benign:3
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at