chr9-101361251-CTA-C

Position:

• chr9-101361251-CTA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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]

(HGNC:):

ACMG classification

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: 7470 AN: 152100 Hom.: 257 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0641

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0749

Gnomad OTH AF: 0.0407

GnomAD4 exome AF: 0.0186 AC: 41 AN: 2206 Hom.: 0 AF XY: 0.0253 AC XY: 29 AN XY: 1148

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.0256

Gnomad4 FIN exome AF: 0.0507

Gnomad4 NFE exome AF: 0.0411

Gnomad4 OTH exome AF: 0.0185

GnomAD4 genome AF: 0.0491 AC: 7472 AN: 152220 Hom.: 257 Cov.: 32 AF XY: 0.0483 AC XY: 3591 AN XY: 74422

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0386

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0641

Gnomad4 NFE AF: 0.0749

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0592 Hom.: 41

Bravo AF: 0.0447

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs35538457; hg19: chr9-104123533;