19-29699249-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_031448.6(C19orf12):c.*3463G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0981 in 450,000 control chromosomes in the GnomAD database, including 3,736 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_031448.6 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.140 AC: 21198AN: 151492Hom.: 2480 Cov.: 30
GnomAD3 exomes AF: 0.0781 AC: 9877AN: 126400Hom.: 657 AF XY: 0.0755 AC XY: 5224AN XY: 69202
GnomAD4 exome AF: 0.0769 AC: 22932AN: 298390Hom.: 1250 Cov.: 0 AF XY: 0.0739 AC XY: 12551AN XY: 169842
GnomAD4 genome AF: 0.140 AC: 21223AN: 151610Hom.: 2486 Cov.: 30 AF XY: 0.135 AC XY: 10012AN XY: 74038
ClinVar
Submissions by phenotype
Neurodegeneration with brain iron accumulation 4 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at