Genetic Variant BAALC:p.Ala35Glu (chr8-103141001-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_024812.3(BAALC):c.104C>A(p.Ala35Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. 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. A35V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

BAALC
NM_024812.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.350

Publications

0 publications found

Variant links:

Genes affected

BAALC (HGNC:14333): (BAALC binder of MAP3K1 and KLF4) This gene was identified by gene expression studies in patients with acute myeloid leukemia (AML). The gene is conserved among mammals and is not found in lower organisms. Tissues that express this gene develop from the neuroectoderm. Multiple alternatively spliced transcript variants that encode different proteins have been described for this gene; however, some of the transcript variants are found only in AML cell lines. [provided by RefSeq, Jul 2008]

BAALC links:

BAALC-AS2 (HGNC:28595): (BAALC antisense RNA 2)

BAALC-AS2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.15965486).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024812.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
BAALC	NM_024812.3	MANE Select	c.104C>A	p.Ala35Glu	missense	Exon 1 of 3	NP_079088.1	Q8WXS3-2
BAALC	NM_001364874.1		c.104C>A	p.Ala35Glu	missense	Exon 1 of 4	NP_001351803.1	Q8WXS3-1
BAALC	NM_001024372.2		c.104C>A	p.Ala35Glu	missense	Exon 1 of 2	NP_001019543.1	Q8WXS3-6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
BAALC	ENST00000309982.10	TSL:1 MANE Select	c.104C>A	p.Ala35Glu	missense	Exon 1 of 3	ENSP00000312457.5	Q8WXS3-2
BAALC	ENST00000438105.2	TSL:1	c.104C>A	p.Ala35Glu	missense	Exon 1 of 2	ENSP00000395024.2	Q8WXS3-6
BAALC-AS2	ENST00000436771.4	TSL:1	n.286+253G>T		intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1372394

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

677194

African (AFR)

AF:

0.00

AC:

AN:

28004

American (AMR)

AF:

0.00

AC:

AN:

33016

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24038

East Asian (EAS)

AF:

0.00

AC:

AN:

32068

South Asian (SAS)

AF:

0.00

AC:

AN:

76832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

47744

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5430

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1068568

Other (OTH)

AF:

0.00

AC:

AN:

56694

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.014

Eigen

Benign

-0.61

Eigen_PC

Benign

-0.67

FATHMM_MKL

Benign

0.21

LIST_S2

Benign

0.63

M_CAP

Pathogenic

0.63

MetaRNN

Benign

0.16

MetaSVM

Benign

-0.98

PhyloP100

0.35

PrimateAI

Pathogenic

0.83

PROVEAN

Benign

-0.80

REVEL

Benign

0.032

Sift

Benign

0.043

Sift4G

Benign

0.58

Polyphen

0.30

Vest4

0.17

MutPred

0.52

Gain of solvent accessibility (P = 0.0246)

MVP

0.26

MPC

0.35

ClinPred

0.88

GERP RS

1.1

PromoterAI

0.067

Neutral

(source)

Varity_R

0.19

gMVP

0.067

Mutation Taster

=91/9

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over