rs1572983

chr9-101371346-C-Gchr9-101371346-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001701.4(BAAT):c.59G>C(p.Arg20Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R20Q) has been classified as Benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: BAAT NM_001701.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAAT	NM_001701.4	c.59G>C	p.Arg20Pro	missense_variant	2/4	ENST00000259407.7
BAAT	NM_001127610.2	c.59G>C	p.Arg20Pro	missense_variant	2/4
BAAT	NM_001374715.1	c.59G>C	p.Arg20Pro	missense_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAAT	ENST00000259407.7	c.59G>C	p.Arg20Pro	missense_variant	2/4	1	NM_001701.4	P1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 72

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.83
BayesDel_addAF	Benign	-0.0054	T
BayesDel_noAF	Benign	-0.25
Cadd	Benign	18
Dann	Benign	0.97
DEOGEN2	Benign	0.20	T;T
Eigen	Benign	-0.66
Eigen_PC	Benign	-0.95
FATHMM_MKL	Benign	0.071	N
M_CAP	Benign	0.062	D
MetaRNN	Uncertain	0.60	D;D
MetaSVM	Uncertain	-0.095	T
MutationAssessor	Pathogenic	3.0	M;M
MutationTaster	Benign	1.0	P;P
PrimateAI	Benign	0.19	T
PROVEAN	Uncertain	-3.3	D;D
REVEL	Uncertain	0.37
Sift	Benign	0.12	T;T
Sift4G	Benign	0.21	T;T
Polyphen		0.98	D;D
Vest4		0.48
MutPred		0.41		Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);
MVP		0.71
MPC		0.31
ClinPred		0.72	D
GERP RS		-3.9
Varity_R		0.95
gMVP		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1572983; hg19: chr9-104133628;