chr19-49861227-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_007254.4(PNKP):c.*21A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00721 in 1,489,272 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_007254.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00481 AC: 732AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00661 AC: 1643AN: 248644Hom.: 12 AF XY: 0.00763 AC XY: 1031AN XY: 135064
GnomAD4 exome AF: 0.00748 AC: 10001AN: 1336984Hom.: 70 Cov.: 20 AF XY: 0.00785 AC XY: 5270AN XY: 671666
GnomAD4 genome AF: 0.00481 AC: 733AN: 152288Hom.: 1 Cov.: 32 AF XY: 0.00495 AC XY: 369AN XY: 74472
ClinVar
Submissions by phenotype
Microcephaly, seizures, and developmental delay 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. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at