chr6-73762742-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_133493.5(CD109):āc.857T>Cā(p.Ile286Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000313 in 1,596,616 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 (ā ).
Frequency
Consequence
NM_133493.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD109 | NM_133493.5 | c.857T>C | p.Ile286Thr | missense_variant, splice_region_variant | 9/33 | ENST00000287097.6 | NP_598000.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD109 | ENST00000287097.6 | c.857T>C | p.Ile286Thr | missense_variant, splice_region_variant | 9/33 | 1 | NM_133493.5 | ENSP00000287097.4 | ||
CD109 | ENST00000437994.6 | c.857T>C | p.Ile286Thr | missense_variant, splice_region_variant | 9/33 | 1 | ENSP00000388062.2 | |||
CD109 | ENST00000422508.6 | c.626T>C | p.Ile209Thr | missense_variant, splice_region_variant | 8/32 | 1 | ENSP00000404475.2 | |||
CD109 | ENST00000649530.1 | n.829T>C | splice_region_variant, non_coding_transcript_exon_variant | 8/26 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000291 AC: 7AN: 240570Hom.: 0 AF XY: 0.0000154 AC XY: 2AN XY: 129998
GnomAD4 exome AF: 0.0000318 AC: 46AN: 1444290Hom.: 0 Cov.: 29 AF XY: 0.0000209 AC XY: 15AN XY: 718742
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2023 | The c.857T>C (p.I286T) alteration is located in exon 9 (coding exon 9) of the CD109 gene. This alteration results from a T to C substitution at nucleotide position 857, causing the isoleucine (I) at amino acid position 286 to be replaced by a threonine (T). 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