6-7541909-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_004415.4(DSP):c.-7C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000561 in 1,603,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004415.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DSP | NM_004415.4 | c.-7C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 24 | ENST00000379802.8 | NP_004406.2 | ||
DSP | NM_004415.4 | c.-7C>T | 5_prime_UTR_variant | Exon 1 of 24 | ENST00000379802.8 | NP_004406.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DSP | ENST00000379802 | c.-7C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 24 | 1 | NM_004415.4 | ENSP00000369129.3 | |||
DSP | ENST00000379802 | c.-7C>T | 5_prime_UTR_variant | Exon 1 of 24 | 1 | NM_004415.4 | ENSP00000369129.3 |
Frequencies
GnomAD3 genomes AF: 0.0000136 AC: 2AN: 146756Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1456448Hom.: 0 Cov.: 30 AF XY: 0.00000690 AC XY: 5AN XY: 724162
GnomAD4 genome AF: 0.0000136 AC: 2AN: 146756Hom.: 0 Cov.: 33 AF XY: 0.0000140 AC XY: 1AN XY: 71482
ClinVar
Submissions by phenotype
Cardiomyopathy Uncertain:1
This variant is located in the 5' untranslated region of the DSP gene. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with DSP-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at