rs61756326

Variant names:

• chr9-101362734-C-T
• rs61756326
• NM_001701.4:c.951G>A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_001701.4(BAAT):​c.951G>A​(p.Gln317Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00644 in 1,614,218 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0039 (5 hom., cov: 32)
  • Exomes 𝑓: 0.0067 (43 hom.)
• Consequence: BAAT NM_001701.4 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -0.705

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 Benign. Variant got -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 9-101362734-C-T is Benign according to our data. Variant chr9-101362734-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 197199.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.705 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAAT	NM_001701.4	c.951G>A	p.Gln317Gln	synonymous_variant	Exon 4 of 4	ENST00000259407.7	NP_001692.1
BAAT	NM_001127610.2	c.951G>A	p.Gln317Gln	synonymous_variant	Exon 4 of 4		NP_001121082.1
BAAT	NM_001374715.1	c.951G>A	p.Gln317Gln	synonymous_variant	Exon 4 of 4		NP_001361644.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAAT	ENST00000259407.7	c.951G>A	p.Gln317Gln	synonymous_variant	Exon 4 of 4	1	NM_001701.4	ENSP00000259407.2

Frequencies

GnomAD3 genomes AF: 0.00388 AC: 590 AN: 152226 Hom.: 5 Cov.: 32

Gnomad AFR AF: 0.00101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000982

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00227

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00723

Gnomad OTH AF: 0.00478

GnomAD3 exomes AF: 0.00413 AC: 1037 AN: 251064 Hom.: 2 AF XY: 0.00414 AC XY: 561 AN XY: 135666

Gnomad AFR exome AF: 0.00135

Gnomad AMR exome AF: 0.00130

Gnomad ASJ exome AF: 0.000993

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00167

Gnomad FIN exome AF: 0.00286

Gnomad NFE exome AF: 0.00725

Gnomad OTH exome AF: 0.00392

GnomAD4 exome AF: 0.00670 AC: 9799 AN: 1461874 Hom.: 43 Cov.: 33 AF XY: 0.00647 AC XY: 4702 AN XY: 727238

Gnomad4 AFR exome AF: 0.000896

Gnomad4 AMR exome AF: 0.00125

Gnomad4 ASJ exome AF: 0.000880

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.00154

Gnomad4 FIN exome AF: 0.00277

Gnomad4 NFE exome AF: 0.00817

Gnomad4 OTH exome AF: 0.00510

GnomAD4 genome AF: 0.00387 AC: 590 AN: 152344 Hom.: 5 Cov.: 32 AF XY: 0.00368 AC XY: 274 AN XY: 74494

Gnomad4 AFR AF: 0.00101

Gnomad4 AMR AF: 0.000980

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00228

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.00723

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00549 Hom.: 3

Bravo AF: 0.00366

EpiCase AF: 0.00562

EpiControl AF: 0.00545

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

May 08, 2015

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

Mar 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

BAAT: BP4, BP7, BS2 -

Nov 21, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hypercholanemia, familial 1 Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.5
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.20		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.20		Position offset: -23

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

Publications

LitVar

Other links and lift over

dbSNP: rs61756326; hg19: chr9-104125016;