chr11-47419207-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002804.5(PSMC3):c.1128-10C>T 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 0.373 in 1,613,228 control chromosomes in the GnomAD database, including 116,159 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_002804.5 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 |
---|---|---|---|---|---|---|---|
PSMC3 | NM_002804.5 | c.1128-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000298852.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMC3 | ENST00000298852.8 | c.1128-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002804.5 | ||||
PSMC3 | ENST00000602866.5 | c.1080-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 | ||||
PSMC3 | ENST00000619920.4 | c.1128-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
PSMC3 | ENST00000530912.5 | c.1002-10C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.309 AC: 47013AN: 151950Hom.: 8179 Cov.: 32
GnomAD3 exomes AF: 0.353 AC: 88425AN: 250172Hom.: 16919 AF XY: 0.369 AC XY: 49836AN XY: 135220
GnomAD4 exome AF: 0.379 AC: 553979AN: 1461160Hom.: 107977 Cov.: 39 AF XY: 0.383 AC XY: 278614AN XY: 726932
GnomAD4 genome AF: 0.309 AC: 47021AN: 152068Hom.: 8182 Cov.: 32 AF XY: 0.306 AC XY: 22767AN XY: 74344
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at