dbSNP rs62527607: BAALC:c.160+264G>T (chr8-103141321-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024812.3(BAALC):c.160+264G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 397,986 control chromosomes in the GnomAD database, including 4,416 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 1520 hom., cov: 33)

Exomes 𝑓: 0.14 ( 2896 hom. )

Consequence

BAALC
NM_024812.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.609

Publications

10 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: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

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	Effect	Exon Rank	Protein	UniProt
BAALC	NM_024812.3	MANE Select	c.160+264G>T	intron	N/A	NP_079088.1	Q8WXS3-2
BAALC	NM_001364874.1		c.160+264G>T	intron	N/A	NP_001351803.1	Q8WXS3-1
BAALC	NM_001024372.2		c.160+264G>T	intron	N/A	NP_001019543.1	Q8WXS3-6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BAALC	ENST00000309982.10	TSL:1 MANE Select	c.160+264G>T	intron	N/A	ENSP00000312457.5	Q8WXS3-2
BAALC	ENST00000438105.2	TSL:1	c.160+264G>T	intron	N/A	ENSP00000395024.2	Q8WXS3-6
BAALC-AS2	ENST00000436771.4	TSL:1	n.219C>A	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.134

AC:

20325

AN:

152024

Hom.:

1522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.0997

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.000969

Gnomad SAS

AF:

0.0784

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.135

GnomAD4 exome

AF:

0.141

AC:

34716

AN:

245844

Hom.:

2896

Cov.:

AF XY:

0.139

AC XY:

17597

AN XY:

126154

show subpopulations

African (AFR)

AF:

0.111

AC:

695

AN:

6250

American (AMR)

AF:

0.0927

AC:

575

AN:

6202

Ashkenazi Jewish (ASJ)

AF:

0.155

AC:

1309

AN:

8424

East Asian (EAS)

AF:

0.000102

AC:

AN:

19700

South Asian (SAS)

AF:

0.0824

AC:

690

AN:

8376

European-Finnish (FIN)

AF:

0.216

AC:

4405

AN:

20408

Middle Eastern (MID)

AF:

0.176

AC:

218

AN:

1242

European-Non Finnish (NFE)

AF:

0.155

AC:

24714

AN:

159572

Other (OTH)

AF:

0.135

AC:

2108

AN:

15670

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1341

2682

4022

5363

6704

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

240

360

480

600

<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:

0.134

AC:

20339

AN:

152142

Hom.:

1520

Cov.:

AF XY:

0.133

AC XY:

9878

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.104

AC:

4307

AN:

41530

American (AMR)

AF:

0.0995

AC:

1522

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

564

AN:

3466

East Asian (EAS)

AF:

0.000971

AC:

AN:

5148

South Asian (SAS)

AF:

0.0785

AC:

378

AN:

4816

European-Finnish (FIN)

AF:

0.222

AC:

2347

AN:

10588

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10839

AN:

67980

Other (OTH)

AF:

0.133

AC:

282

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

901

1802

2704

3605

4506

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.136

Hom.:

534

Bravo

AF:

0.124

Asia WGS

AF:

0.0400

AC:

141

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.055

(source)

DANN

Benign

0.78

PhyloP100

-0.61

PromoterAI

-0.019

Neutral

(source)

Mutation Taster

=100/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over