7-107891209-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000108.5(DLD):c.-42C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000288 in 1,460,364 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000108.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLD | NM_000108.5 | c.-42C>T | 5_prime_UTR_variant | Exon 1 of 14 | ENST00000205402.10 | NP_000099.2 | ||
DLD | NM_001289751.1 | c.-42C>T | 5_prime_UTR_variant | Exon 1 of 13 | NP_001276680.1 | |||
DLD | NM_001289752.1 | c.-42C>T | 5_prime_UTR_variant | Exon 1 of 13 | NP_001276681.1 | |||
DLD | NM_001289750.1 | c.-190C>T | 5_prime_UTR_variant | Exon 1 of 12 | NP_001276679.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 exomes AF: 0.0000680 AC: 17AN: 250036Hom.: 1 AF XY: 0.0000517 AC XY: 7AN XY: 135394
GnomAD4 exome AF: 0.0000288 AC: 42AN: 1460364Hom.: 1 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 726528
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at