Variant 9-101360970-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001701.4(BAAT):c.*1458G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 166,802 control chromosomes in the GnomAD database, including 2,130 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 1989 hom., cov: 32)

Exomes 𝑓: 0.13 ( 141 hom. )

Consequence

BAAT
NM_001701.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.291

Variant links:

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]

BAAT links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 9-101360970-C-T is Benign according to our data. Variant chr9-101360970-C-T is described in ClinVar as [Benign]. Clinvar id is 364254.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
BAAT	NM_001701.4 linkuse as main transcript	c.*1458G>A	3_prime_UTR_variant	4/4	ENST00000259407.7
BAAT	NM_001127610.2 linkuse as main transcript	c.*1458G>A	3_prime_UTR_variant	4/4
BAAT	NM_001374715.1 linkuse as main transcript	c.*1458G>A	3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
BAAT	ENST00000259407.7 linkuse as main transcript	c.*1458G>A	3_prime_UTR_variant	4/4	1	NM_001701.4	P1
	ENST00000447628.2 linkuse as main transcript	n.1308C>T	non_coding_transcript_exon_variant	3/3
BAAT	ENST00000674791.1 linkuse as main transcript	c.762+1953G>A	intron_variant, NMD_transcript_variant
BAAT	ENST00000674909.1 linkuse as main transcript	c.804+1911G>A	intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.154

AC:

23438

AN:

151980

Hom.:

1985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0478

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.0902

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.148

GnomAD4 exome

AF:

0.128

AC:

1877

AN:

14704

Hom.:

141

Cov.:

AF XY:

0.129

AC XY:

1063

AN XY:

8238

show subpopulations

Gnomad4 AFR exome

AF:

0.222

Gnomad4 AMR exome

AF:

0.132

Gnomad4 ASJ exome

AF:

0.114

Gnomad4 EAS exome

AF:

0.0519

Gnomad4 SAS exome

AF:

0.158

Gnomad4 FIN exome

AF:

0.0981

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.162

GnomAD4 genome

AF:

0.154

AC:

23465

AN:

152098

Hom.:

1989

Cov.:

AF XY:

0.152

AC XY:

11268

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.202

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.119

Gnomad4 EAS

AF:

0.0479

Gnomad4 SAS

AF:

0.183

Gnomad4 FIN

AF:

0.0902

Gnomad4 NFE

AF:

0.146

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.145

Hom.:

323

Bravo

AF:

0.157

Asia WGS

AF:

0.122

AC:

424

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hypercholanemia, familial 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

7.7

DANN

Benign

0.49

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over