3-160257415-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020800.3(IFT80):c.*1110A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 152,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020800.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFT80 | ENST00000326448 | c.*1110A>G | 3_prime_UTR_variant | Exon 20 of 20 | 1 | NM_020800.3 | ENSP00000312778.7 | |||
IFT80 | ENST00000483465 | c.*1110A>G | 3_prime_UTR_variant | Exon 19 of 19 | 1 | ENSP00000418196.1 | ||||
ENSG00000248710 | ENST00000483754.1 | n.*58+1052A>G | intron_variant | Intron 18 of 18 | 2 | ENSP00000456272.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 0
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74422
ClinVar
Submissions by phenotype
Asphyxiating thoracic dystrophy 2 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at