3-160268478-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020800.3(IFT80):c.2158C>A(p.Gln720Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000211 in 1,613,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_020800.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IFT80 | ENST00000326448.12 | c.2158C>A | p.Gln720Lys | missense_variant | Exon 19 of 20 | 1 | NM_020800.3 | ENSP00000312778.7 | ||
ENSG00000248710 | ENST00000483754.1 | n.2671C>A | non_coding_transcript_exon_variant | Exon 17 of 19 | 2 | ENSP00000456272.1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000223 AC: 56AN: 251092Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135702
GnomAD4 exome AF: 0.000211 AC: 308AN: 1461000Hom.: 0 Cov.: 30 AF XY: 0.000213 AC XY: 155AN XY: 726848
GnomAD4 genome AF: 0.000210 AC: 32AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74444
ClinVar
Submissions by phenotype
Asphyxiating thoracic dystrophy 2 Uncertain:2
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The IFT80 c.2158C>A; p.Gln720Lys variant (rs201820395), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 501586). This variant is found in the general population with an overall allele frequency of 0.021 % (59/282,490 alleles) in the Genome Aggregation Database. The glutamine at codon 720 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.178). Due to limited information, the clinical significance of this variant is uncertain at this time. -
not provided Uncertain:1
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Jeune thoracic dystrophy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at