9-101361112-T-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001701.4(BAAT):c.*1316A>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.000112 in 151,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
BAAT
NM_001701.4 3_prime_UTR
NM_001701.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.03
Genes affected
BAAT (HGNC:932): (bile acid-CoA:amino acid N-acyltransferase) The protein encoded by this gene is a liver enzyme that catalyzes the transfer of C24 bile acids from the acyl-CoA thioester to either glycine or taurine, the second step in the formation of bile acid-amino acid conjugates. The bile acid conjugates then act as a detergent in the gastrointestinal tract, which enhances lipid and fat-soluble vitamin absorption. Defects in this gene are a cause of familial hypercholanemia (FHCA). Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAAT | NM_001701.4 | c.*1316A>C | 3_prime_UTR_variant | 4/4 | ENST00000259407.7 | ||
BAAT | NM_001127610.2 | c.*1316A>C | 3_prime_UTR_variant | 4/4 | |||
BAAT | NM_001374715.1 | c.*1316A>C | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAAT | ENST00000259407.7 | c.*1316A>C | 3_prime_UTR_variant | 4/4 | 1 | NM_001701.4 | P1 | ||
ENST00000447628.2 | n.1450T>G | non_coding_transcript_exon_variant | 3/3 | ||||||
BAAT | ENST00000674791.1 | c.762+1811A>C | intron_variant, NMD_transcript_variant | ||||||
BAAT | ENST00000674909.1 | c.804+1769A>C | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151678Hom.: 0 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 4168Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2192
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GnomAD4 genome AF: 0.000112 AC: 17AN: 151678Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74108
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypercholanemia, familial Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at