chr20-49230200-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_017895.8(DDX27):c.882C>T(p.Gly294=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000578 in 1,610,292 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 Likely benign (★).
Frequency
Consequence
NM_017895.8 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDX27 | NM_017895.8 | c.882C>T | p.Gly294= | splice_region_variant, synonymous_variant | 9/21 | ENST00000618172.5 | |
DDX27 | NM_001348187.2 | c.882C>T | p.Gly294= | splice_region_variant, synonymous_variant | 9/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDX27 | ENST00000618172.5 | c.882C>T | p.Gly294= | splice_region_variant, synonymous_variant | 9/21 | 1 | NM_017895.8 | P1 | |
DDX27 | ENST00000484427.5 | n.984C>T | splice_region_variant, non_coding_transcript_exon_variant | 9/19 | 1 | ||||
DDX27 | ENST00000493252.2 | c.408C>T | p.Gly136= | splice_region_variant, synonymous_variant | 5/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000930 AC: 23AN: 247272Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 133806
GnomAD4 exome AF: 0.0000597 AC: 87AN: 1457980Hom.: 0 Cov.: 31 AF XY: 0.0000745 AC XY: 54AN XY: 725284
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74482
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at