8-78738498-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000880.4(IL7):c.360+6C>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 0.00158 in 1,610,184 control chromosomes in the GnomAD database, including 65 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 Uncertain significance (★).
Frequency
Consequence
NM_000880.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00171 AC: 260AN: 152152Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00458 AC: 1137AN: 247994Hom.: 24 AF XY: 0.00440 AC XY: 590AN XY: 133980
GnomAD4 exome AF: 0.00157 AC: 2292AN: 1457914Hom.: 56 Cov.: 29 AF XY: 0.00153 AC XY: 1108AN XY: 725230
GnomAD4 genome AF: 0.00169 AC: 258AN: 152270Hom.: 9 Cov.: 32 AF XY: 0.00171 AC XY: 127AN XY: 74458
ClinVar
Submissions by phenotype
Epidermodysplasia verruciformis, susceptibility to, 5 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 15, 2024 | - - |
IL7-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 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