9-137192305-AGCGCCTGCTCCT-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_001128228.3(TPRN):c.2015_2026delAGGAGCAGGCGC(p.Gln672_Ala675del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000274 in 1,460,658 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001128228.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPRN | ENST00000409012.6 | c.2015_2026delAGGAGCAGGCGC | p.Gln672_Ala675del | disruptive_inframe_deletion | Exon 3 of 4 | 1 | NM_001128228.3 | ENSP00000387100.4 | ||
TPRN | ENST00000477345.1 | n.2736_2747delAGGAGCAGGCGC | non_coding_transcript_exon_variant | Exon 2 of 3 | 1 | |||||
TPRN | ENST00000333046.8 | c.1409_1420delAGGAGCAGGCGC | p.Gln470_Ala473del | disruptive_inframe_deletion | Exon 3 of 3 | 2 | ENSP00000327617.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460658Hom.: 0 AF XY: 0.00000275 AC XY: 2AN XY: 726642
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
In-frame deletion of 4 amino acids in a non-repeat region; Not observed at significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at