rs2229594

Variant names:

• chr9-101362382-C-T
• rs2229594
• NM_001701.4:c.*46G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-101362382-C-T
• chr9-101362382-C-G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001701.4(BAAT):​c.*46G>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 0.812 in 1,581,680 control chromosomes in the GnomAD database, including 524,539 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.78 (46941 hom., cov: 31)
  • Exomes 𝑓: 0.82 (477598 hom.)
• Consequence: BAAT NM_001701.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -0.284
• Publications: 17 publications found

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: Unknown, AR Classification: SUPPORTIVE, LIMITED Submitted by: Laboratory for Molecular Medicine, Orphanet
• bile acid conjugation defect 1

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 9-101362382-C-T is Benign according to our data. Variant chr9-101362382-C-T is described in ClinVar as Benign. ClinVar VariationId is 364275.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001701.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAAT	NM_001701.4	MANE Select	c.*46G>A		3_prime_UTR	Exon 4 of 4	NP_001692.1	Q14032
	BAAT	NM_001127610.2		c.*46G>A		3_prime_UTR	Exon 4 of 4	NP_001121082.1	Q14032
	BAAT	NM_001374715.1		c.*46G>A		3_prime_UTR	Exon 4 of 4	NP_001361644.1	Q14032

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAAT	ENST00000259407.7	TSL:1 MANE Select	c.*46G>A		3_prime_UTR	Exon 4 of 4	ENSP00000259407.2	Q14032
	BAAT	ENST00000395051.4	TSL:1	c.*46G>A		3_prime_UTR	Exon 4 of 4	ENSP00000378491.3	Q14032
	BAAT	ENST00000904170.1		c.*46G>A		3_prime_UTR	Exon 5 of 5	ENSP00000574229.1

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118953 AN: 151916 Hom.: 46910 Cov.: 31

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.810

GnomAD2 exomes AF: 0.784 AC: 188491 AN: 240452 AF XY: 0.785

Gnomad AFR exome AF: 0.708

Gnomad AMR exome AF: 0.724

Gnomad ASJ exome AF: 0.823

Gnomad EAS exome AF: 0.653

Gnomad FIN exome AF: 0.859

Gnomad NFE exome AF: 0.839

Gnomad OTH exome AF: 0.812

GnomAD4 exome AF: 0.815 AC: 1165837 AN: 1429646 Hom.: 477598 Cov.: 27 AF XY: 0.813 AC XY: 579523 AN XY: 712470

African (AFR) AF: 0.703 AC: 23048 AN: 32802

American (AMR) AF: 0.731 AC: 32066 AN: 43888

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 21108 AN: 25820

East Asian (EAS) AF: 0.647 AC: 25478 AN: 39408

South Asian (SAS) AF: 0.701 AC: 59486 AN: 84876

European-Finnish (FIN) AF: 0.856 AC: 44588 AN: 52082

Middle Eastern (MID) AF: 0.849 AC: 4440 AN: 5228

European-Non Finnish (NFE) AF: 0.836 AC: 907905 AN: 1086186

Other (OTH) AF: 0.804 AC: 47718 AN: 59356

GnomAD4 genome AF: 0.783 AC: 119023 AN: 152034 Hom.: 46941 Cov.: 31 AF XY: 0.781 AC XY: 58018 AN XY: 74306

African (AFR) AF: 0.706 AC: 29263 AN: 41444

American (AMR) AF: 0.765 AC: 11664 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2872 AN: 3466

East Asian (EAS) AF: 0.650 AC: 3349 AN: 5156

South Asian (SAS) AF: 0.680 AC: 3280 AN: 4824

European-Finnish (FIN) AF: 0.852 AC: 9009 AN: 10580

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56888 AN: 67998

Other (OTH) AF: 0.802 AC: 1692 AN: 2110

Alfa AF: 0.817 Hom.: 90576

Bravo AF: 0.774

Asia WGS AF: 0.666 AC: 2315 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	Hypercholanemia, familial 1 (2)
-	-	2	not provided (2)
-	-	1	Bile acid conjugation defect 1 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.71
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2229594; hg19: chr9-104124664; COSMIC: COSV52291743; COSMIC: COSV52291743;