chr22-30375469-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001017437.5(CCDC157):c.1673-10T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,613,174 control chromosomes in the GnomAD database, including 41,915 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001017437.5 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC157 | NM_001017437.5 | c.1673-10T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000338306.8 | |||
KIAA1656 | NR_046312.1 | n.947A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC157 | ENST00000338306.8 | c.1673-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001017437.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.203 AC: 30857AN: 152050Hom.: 3389 Cov.: 31
GnomAD3 exomes AF: 0.197 AC: 49475AN: 250944Hom.: 5442 AF XY: 0.199 AC XY: 27014AN XY: 135642
GnomAD4 exome AF: 0.224 AC: 327147AN: 1461008Hom.: 38526 Cov.: 31 AF XY: 0.222 AC XY: 161005AN XY: 726828
GnomAD4 genome AF: 0.203 AC: 30857AN: 152166Hom.: 3389 Cov.: 31 AF XY: 0.196 AC XY: 14572AN XY: 74398
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at