19-44929263-G-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_028412.1(APOC1P1):n.552+1333G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00817 in 148,584 control chromosomes in the GnomAD database, including 26 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
Genomes: 𝑓 0.0082 ( 26 hom., cov: 30)
Consequence
APOC1P1
NR_028412.1 intron, non_coding_transcript
NR_028412.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.162
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00817 (1214/148584) while in subpopulation AFR AF= 0.0287 (1157/40270). AF 95% confidence interval is 0.0274. There are 26 homozygotes in gnomad4. There are 556 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 26 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APOC1P1 | NR_028412.1 | n.552+1333G>T | intron_variant, non_coding_transcript_variant | ||||
APOC1P1 | NR_028413.1 | n.367+1333G>T | intron_variant, non_coding_transcript_variant | ||||
APOC1P1 | NR_028414.1 | n.244+1333G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APOC1P1 | ENST00000571466.3 | n.194+1333G>T | intron_variant, non_coding_transcript_variant | ||||||
APOC1P1 | ENST00000701959.1 | n.245+1333G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00815 AC: 1210AN: 148490Hom.: 26 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00817 AC: 1214AN: 148584Hom.: 26 Cov.: 30 AF XY: 0.00769 AC XY: 556AN XY: 72332
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at