rs1162389472
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018051.5(DYNC2I1):c.3169G>A(p.Ala1057Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000818 in 1,589,528 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 Uncertain significance (★).
Frequency
Consequence
NM_018051.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DYNC2I1 | NM_018051.5 | c.3169G>A | p.Ala1057Thr | missense_variant | 25/25 | ENST00000407559.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DYNC2I1 | ENST00000407559.8 | c.3169G>A | p.Ala1057Thr | missense_variant | 25/25 | 1 | NM_018051.5 | P1 | |
DYNC2I1 | ENST00000444851.5 | c.*758G>A | 3_prime_UTR_variant, NMD_transcript_variant | 20/20 | 1 | ||||
DYNC2I1 | ENST00000467220.1 | n.4968G>A | non_coding_transcript_exon_variant | 20/20 | 2 | ||||
DYNC2I1 | ENST00000454771.1 | c.559G>A | p.Ala187Thr | missense_variant, NMD_transcript_variant | 4/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152264Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000835 AC: 12AN: 1437264Hom.: 0 Cov.: 31 AF XY: 0.00000702 AC XY: 5AN XY: 712188
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
Short-rib thoracic dysplasia 8 with or without polydactyly Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 05, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 474630). This variant has not been reported in the literature in individuals affected with WDR60-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1057 of the WDR60 protein (p.Ala1057Thr). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at