13-20631001-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006531.5(IFT88):c.1300-15A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 1,462,846 control chromosomes in the GnomAD database, including 400,386 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006531.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IFT88 | NM_006531.5 | c.1300-15A>T | intron_variant | Intron 15 of 25 | ENST00000351808.10 | NP_006522.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.696 AC: 105641AN: 151826Hom.: 37800 Cov.: 31
GnomAD3 exomes AF: 0.770 AC: 192903AN: 250504Hom.: 75893 AF XY: 0.774 AC XY: 104886AN XY: 135436
GnomAD4 exome AF: 0.740 AC: 969548AN: 1310902Hom.: 362570 Cov.: 19 AF XY: 0.745 AC XY: 492163AN XY: 660512
GnomAD4 genome AF: 0.696 AC: 105703AN: 151944Hom.: 37816 Cov.: 31 AF XY: 0.705 AC XY: 52309AN XY: 74240
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at