11-31785543-CTT-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_019040.5(ELP4):c.*2022_*2023delTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000886 in 191,952 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019040.5 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELP4 | NM_019040.5 | c.*2022_*2023delTT | 3_prime_UTR_variant | Exon 10 of 10 | ENST00000640961.2 | NP_061913.3 | ||
ELP4 | NM_001288726.2 | c.*2117_*2118delTT | 3_prime_UTR_variant | Exon 12 of 12 | NP_001275655.1 | |||
ELP4 | NM_001288725.2 | c.*2008_*2009delTT | 3_prime_UTR_variant | Exon 11 of 11 | NP_001275654.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000856 AC: 13AN: 151954Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.000100 AC: 4AN: 39880Hom.: 0 AF XY: 0.000109 AC XY: 2AN XY: 18356
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152072Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74328
ClinVar
Submissions by phenotype
Aniridia 1;C0344559:Irido-corneo-trabecular dysgenesis Uncertain:1
This variant occurs in a non-coding region of the PAX6 gene. It does not change the encoded amino acid sequence of the PAX6 protein. This variant is present in population databases (rs777790874, gnomAD 0.03%). This variant has been observed in individual(s) with aniridia (PMID: 30291432). ClinVar contains an entry for this variant (Variation ID: 1468159). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at