chr20-32985091-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080675.4(SUN5):c.984+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000362 in 1,612,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080675.4 splice_region, intron
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 |
---|---|---|---|---|---|---|---|
SUN5 | NM_080675.4 | c.984+8C>T | splice_region_variant, intron_variant | ENST00000356173.8 | |||
SUN5 | XM_011528573.2 | c.1053+8C>T | splice_region_variant, intron_variant | ||||
SUN5 | XM_011528574.2 | c.909+8C>T | splice_region_variant, intron_variant | ||||
SUN5 | XM_011528575.2 | c.714+8C>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUN5 | ENST00000356173.8 | c.984+8C>T | splice_region_variant, intron_variant | 1 | NM_080675.4 | P2 | |||
SUN5 | ENST00000375523.7 | c.909+8C>T | splice_region_variant, intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000282 AC: 71AN: 251328Hom.: 0 AF XY: 0.000287 AC XY: 39AN XY: 135826
GnomAD4 exome AF: 0.000378 AC: 552AN: 1460384Hom.: 0 Cov.: 31 AF XY: 0.000367 AC XY: 267AN XY: 726540
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74424
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at