chr20-32983828-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_080675.4(SUN5):c.1106A>C(p.Gln369Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000254 in 1,576,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080675.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUN5 | NM_080675.4 | c.1106A>C | p.Gln369Pro | missense_variant | 13/13 | ENST00000356173.8 | |
SUN5 | XM_011528573.2 | c.1175A>C | p.Gln392Pro | missense_variant | 14/14 | ||
SUN5 | XM_011528574.2 | c.1031A>C | p.Gln344Pro | missense_variant | 12/12 | ||
SUN5 | XM_011528575.2 | c.836A>C | p.Gln279Pro | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUN5 | ENST00000356173.8 | c.1106A>C | p.Gln369Pro | missense_variant | 13/13 | 1 | NM_080675.4 | P2 | |
SUN5 | ENST00000375523.7 | c.1031A>C | p.Gln344Pro | missense_variant | 12/12 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000435 AC: 1AN: 230132Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 124654
GnomAD4 exome AF: 0.00000211 AC: 3AN: 1424340Hom.: 0 Cov.: 31 AF XY: 0.00000142 AC XY: 1AN XY: 705702
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.1106A>C (p.Q369P) alteration is located in exon 13 (coding exon 13) of the SUN5 gene. This alteration results from a A to C substitution at nucleotide position 1106, causing the glutamine (Q) at amino acid position 369 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at