13-20568002-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000319980.10(IFT88):c.21+5C>T variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00114 in 713,254 control chromosomes in the GnomAD database, including 3 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 Likely benign (★).
Frequency
Consequence
ENST00000319980.10 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFT88 | NM_006531.5 | c.-7+746C>T | intron_variant | ENST00000351808.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFT88 | ENST00000351808.10 | c.-7+746C>T | intron_variant | 1 | NM_006531.5 | P1 | |||
IFT88 | ENST00000319980.10 | c.21+5C>T | splice_donor_5th_base_variant, intron_variant | 1 | |||||
IFT88 | ENST00000389373.3 | c.-7+5C>T | splice_donor_5th_base_variant, intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000825 AC: 125AN: 151534Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00101 AC: 150AN: 149048Hom.: 0 AF XY: 0.000899 AC XY: 71AN XY: 78934
GnomAD4 exome AF: 0.00123 AC: 690AN: 561612Hom.: 3 Cov.: 0 AF XY: 0.00129 AC XY: 391AN XY: 303370
GnomAD4 genome AF: 0.000824 AC: 125AN: 151642Hom.: 0 Cov.: 32 AF XY: 0.000675 AC XY: 50AN XY: 74070
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at