chr17-67825793-C-CCCGCCGCCA
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_182641.4(BPTF):c.78_86dup(p.Pro29_Pro31dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000678 in 147,558 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A23A) has been classified as Likely benign.
Frequency
Consequence
NM_182641.4 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BPTF | NM_182641.4 | c.78_86dup | p.Pro29_Pro31dup | inframe_insertion | 1/28 | ENST00000306378.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPTF | ENST00000306378.11 | c.78_86dup | p.Pro29_Pro31dup | inframe_insertion | 1/28 | 1 | NM_182641.4 | ||
BPTF | ENST00000321892.8 | c.78_86dup | p.Pro29_Pro31dup | inframe_insertion | 1/30 | 5 | |||
BPTF | ENST00000544778.6 | c.78_86dup | p.Pro29_Pro31dup | inframe_insertion | 1/22 | 5 | |||
BPTF | ENST00000582467.2 | c.78_86dup | p.Pro29_Pro31dup | inframe_insertion | 1/32 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000678 AC: 10AN: 147558Hom.: 0 Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000901 AC: 8AN: 887446Hom.: 0 Cov.: 30 AF XY: 0.00000482 AC XY: 2AN XY: 414642
GnomAD4 genome AF: 0.0000678 AC: 10AN: 147558Hom.: 0 Cov.: 30 AF XY: 0.0000418 AC XY: 3AN XY: 71832
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant, c.78_86dup, results in the insertion of 3 amino acid(s) of the BPTF protein (p.Pro29_Pro31dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with BPTF-related conditions. ClinVar contains an entry for this variant (Variation ID: 1971972). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at