9-101361251-CTA-C
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001701.4(BAAT):c.*1175_*1176del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0487 in 154,426 control chromosomes in the GnomAD database, including 257 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.049 ( 257 hom., cov: 32)
Exomes 𝑓: 0.019 ( 0 hom. )
Consequence
BAAT
NM_001701.4 3_prime_UTR
NM_001701.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.857
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 9-101361251-CTA-C is Benign according to our data. Variant chr9-101361251-CTA-C is described in ClinVar as [Likely_benign]. Clinvar id is 364258.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0732 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BAAT | NM_001701.4 | c.*1175_*1176del | 3_prime_UTR_variant | 4/4 | ENST00000259407.7 | ||
BAAT | NM_001127610.2 | c.*1175_*1176del | 3_prime_UTR_variant | 4/4 | |||
BAAT | NM_001374715.1 | c.*1175_*1176del | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BAAT | ENST00000259407.7 | c.*1175_*1176del | 3_prime_UTR_variant | 4/4 | 1 | NM_001701.4 | P1 | ||
BAAT | ENST00000674791.1 | c.762+1670_762+1671del | intron_variant, NMD_transcript_variant | ||||||
BAAT | ENST00000674909.1 | c.804+1628_804+1629del | intron_variant, NMD_transcript_variant | ||||||
ENST00000447628.2 | downstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0491 AC: 7470AN: 152100Hom.: 257 Cov.: 32
GnomAD3 genomes
AF:
AC:
7470
AN:
152100
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0186 AC: 41AN: 2206Hom.: 0 AF XY: 0.0253 AC XY: 29AN XY: 1148
GnomAD4 exome
AF:
AC:
41
AN:
2206
Hom.:
AF XY:
AC XY:
29
AN XY:
1148
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0491 AC: 7472AN: 152220Hom.: 257 Cov.: 32 AF XY: 0.0483 AC XY: 3591AN XY: 74422
GnomAD4 genome
AF:
AC:
7472
AN:
152220
Hom.:
Cov.:
32
AF XY:
AC XY:
3591
AN XY:
74422
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
37
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypercholanemia, familial Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at