chr22-32445713-G-GAAA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_174932.3(BPIFC):c.531-16_531-15insTTT 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 0.116 in 615,060 control chromosomes in the GnomAD database, including 2,161 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.17 ( 1466 hom., cov: 0)
Exomes 𝑓: 0.12 ( 2161 hom. )
Failed GnomAD Quality Control
Consequence
BPIFC
NM_174932.3 splice_polypyrimidine_tract, intron
NM_174932.3 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0980
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 22-32445713-G-GAAA is Benign according to our data. Variant chr22-32445713-G-GAAA is described in ClinVar as [Benign]. Clinvar id is 2975955.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BPIFC | NM_174932.3 | c.531-16_531-15insTTT | splice_polypyrimidine_tract_variant, intron_variant | ENST00000300399.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BPIFC | ENST00000300399.9 | c.531-16_531-15insTTT | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_174932.3 | P1 | |||
BPIFC | ENST00000397452.5 | c.531-16_531-15insTTT | splice_polypyrimidine_tract_variant, intron_variant | 5 | P1 | ||||
BPIFC | ENST00000534972.4 | c.*236-16_*236-15insTTT | splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.169 AC: 12913AN: 76340Hom.: 1465 Cov.: 0
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GnomAD4 exome AF: 0.116 AC: 71410AN: 615060Hom.: 2161 Cov.: 25 AF XY: 0.117 AC XY: 36382AN XY: 311036
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.169 AC: 12918AN: 76356Hom.: 1466 Cov.: 0 AF XY: 0.170 AC XY: 5705AN XY: 33564
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 08, 2024 | - - |
Computational scores
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Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at