chr7-29400536-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_004067.4(CHN2):c.291-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000592 in 1,612,928 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_004067.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHN2 | NM_004067.4 | c.291-7C>T | splice_region_variant, intron_variant | Intron 5 of 12 | ENST00000222792.11 | NP_004058.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000874 AC: 133AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00149 AC: 374AN: 250576Hom.: 3 AF XY: 0.00142 AC XY: 192AN XY: 135436
GnomAD4 exome AF: 0.000563 AC: 823AN: 1460626Hom.: 4 Cov.: 30 AF XY: 0.000535 AC XY: 389AN XY: 726566
GnomAD4 genome AF: 0.000867 AC: 132AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.00107 AC XY: 80AN XY: 74482
ClinVar
Submissions by phenotype
CHN2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at