chr9-101368187-C-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001701.4(BAAT):c.602G>C(p.Arg201Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,584,312 control chromosomes in the GnomAD database, including 19,486 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R201H) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.16 ( 2058 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17428 hom. )

Consequence

BAAT
NM_001701.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.25

Publications

16 publications found

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 Gene-Disease associations (from GenCC):

hypercholanemia, familial 1
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
bile acid CoA:amino acid N-acyltransferase deficiency
Inheritance: AR Classification: MODERATE Submitted by: ClinGen
familial hypercholanemia
Inheritance: AR, Unknown Classification: SUPPORTIVE, LIMITED Submitted by: Orphanet, Laboratory for Molecular Medicine
bile acid conjugation defect 1
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

BAAT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0026787817).

BP6

Variant 9-101368187-C-G is Benign according to our data. Variant chr9-101368187-C-G is described in ClinVar as Benign. ClinVar VariationId is 258173.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAAT	NM_001701.4 link	c.602G>C	p.Arg201Pro	missense_variant	Exon 3 of 4	ENST00000259407.7	NP_001692.1	Q14032
BAAT	NM_001127610.2 link	c.602G>C	p.Arg201Pro	missense_variant	Exon 3 of 4		NP_001121082.1	Q14032
BAAT	NM_001374715.1 link	c.602G>C	p.Arg201Pro	missense_variant	Exon 3 of 4		NP_001361644.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAAT	ENST00000259407.7 link	c.602G>C	p.Arg201Pro	missense_variant	Exon 3 of 4	1	NM_001701.4	ENSP00000259407.2		Q14032

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

23803

AN:

150986

Hom.:

2052

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.0500

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.0905

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.148

GnomAD2 exomes

AF:

0.139

AC:

35061

AN:

251358

AF XY:

0.143

show subpopulations

Gnomad AFR exome

AF:

0.219

Gnomad AMR exome

AF:

0.130

Gnomad ASJ exome

AF:

0.119

Gnomad EAS exome

AF:

0.0431

Gnomad FIN exome

AF:

0.0979

Gnomad NFE exome

AF:

0.143

Gnomad OTH exome

AF:

0.140

GnomAD4 exome

AF:

0.154

AC:

220990

AN:

1433190

Hom.:

17428

Cov.:

AF XY:

0.155

AC XY:

110761

AN XY:

713670

show subpopulations

African (AFR)

AF:

0.219

AC:

7135

AN:

32562

American (AMR)

AF:

0.135

AC:

5942

AN:

43914

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

3062

AN:

24524

East Asian (EAS)

AF:

0.0794

AC:

2895

AN:

36440

South Asian (SAS)

AF:

0.188

AC:

16137

AN:

86052

European-Finnish (FIN)

AF:

0.104

AC:

5254

AN:

50552

Middle Eastern (MID)

AF:

0.199

AC:

1105

AN:

5558

European-Non Finnish (NFE)

AF:

0.156

AC:

170533

AN:

1095400

Other (OTH)

AF:

0.153

AC:

8927

AN:

58188

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

10736

21472

32209

42945

53681

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6286

12572

18858

25144

31430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.158

AC:

23836

AN:

151122

Hom.:

2058

Cov.:

AF XY:

0.155

AC XY:

11430

AN XY:

73874

show subpopulations

African (AFR)

AF:

0.212

AC:

8754

AN:

41302

American (AMR)

AF:

0.145

AC:

2201

AN:

15148

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

414

AN:

3470

East Asian (EAS)

AF:

0.0501

AC:

246

AN:

4912

South Asian (SAS)

AF:

0.192

AC:

884

AN:

4614

European-Finnish (FIN)

AF:

0.0905

AC:

956

AN:

10566

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.147

AC:

9934

AN:

67802

Other (OTH)

AF:

0.148

AC:

311

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1007

2014

3020

4027

5034

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

270

540

810

1080

1350

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.132

Hom.:

1081

Bravo

AF:

0.160

TwinsUK

AF:

0.158

AC:

585

ALSPAC

AF:

0.155

AC:

596

ESP6500AA

AF:

0.217

AC:

957

ESP6500EA

AF:

0.145

AC:

1250

ExAC

AF:

0.142

AC:

17255

EpiCase

AF:

0.149

EpiControl

AF:

0.149

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jun 09, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hypercholanemia, familial 1

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.75

CADD

Benign

1.2

(source)

DANN

Benign

0.88

DEOGEN2

Benign

0.019

T;T

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.020

MetaRNN

Benign

0.0027

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.67

N;N

PhyloP100

-1.3

PrimateAI

Benign

0.19

PROVEAN

Benign

-0.53

N;N

REVEL

Benign

0.031

Sift

Benign

0.090

T;T

Sift4G

Benign

0.16

T;T

Polyphen

0.0

B;B

Vest4

0.052

MPC

0.059

ClinPred

0.00061

GERP RS

-3.1

Varity_R

0.087

gMVP

0.55

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over