7-158934539-C-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_018051.5(DYNC2I1):c.2768C>A(p.Pro923Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00292 in 1,551,660 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_018051.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DYNC2I1 | NM_018051.5 | c.2768C>A | p.Pro923Gln | missense_variant | Exon 23 of 25 | ENST00000407559.8 | NP_060521.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00262 AC: 398AN: 152072Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00251 AC: 399AN: 158718Hom.: 0 AF XY: 0.00220 AC XY: 183AN XY: 83214
GnomAD4 exome AF: 0.00295 AC: 4126AN: 1399472Hom.: 13 Cov.: 32 AF XY: 0.00288 AC XY: 1985AN XY: 690246
GnomAD4 genome AF: 0.00262 AC: 398AN: 152188Hom.: 1 Cov.: 33 AF XY: 0.00276 AC XY: 205AN XY: 74400
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2768C>A (p.P923Q) alteration is located in exon 23 (coding exon 23) of the WDR60 gene. This alteration results from a C to A substitution at nucleotide position 2768, causing the proline (P) at amino acid position 923 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
DYNC2I1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Short-rib thoracic dysplasia 8 with or without polydactyly Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at