rs2201369

Variant names:

• chr8-103209797-T-C
• rs2201369
• NM_024812.3:c.161-3122T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024812.3(BAALC):​c.161-3122T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,264 control chromosomes in the GnomAD database, including 1,738 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 0.14 (1738 hom., cov: 32)
• Consequence: BAALC NM_024812.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 6 publications found

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-AS1 (HGNC:50461): (BAALC antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAALC	NM_024812.3	c.161-3122T>C		intron_variant	Intron 1 of 2	ENST00000309982.10	NP_079088.1
BAALC	NM_001364874.1	c.266-3122T>C		intron_variant	Intron 2 of 3		NP_001351803.1
BAALC	NM_001024372.2	c.161-18192T>C		intron_variant	Intron 1 of 1		NP_001019543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAALC	ENST00000309982.10	c.161-3122T>C		intron_variant	Intron 1 of 2	1	NM_024812.3	ENSP00000312457.5

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21120 AN: 152146 Hom.: 1740 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.0952

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0708

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.138

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.139 AC: 21128 AN: 152264 Hom.: 1738 Cov.: 32 AF XY: 0.139 AC XY: 10364 AN XY: 74456

African (AFR) AF: 0.0667 AC: 2770 AN: 41542

American (AMR) AF: 0.0950 AC: 1454 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3472

East Asian (EAS) AF: 0.0708 AC: 367 AN: 5186

South Asian (SAS) AF: 0.232 AC: 1122 AN: 4828

European-Finnish (FIN) AF: 0.182 AC: 1930 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12233 AN: 68014

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.170 Hom.: 4236

Bravo AF: 0.130

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.79
PhyloP100		1.2
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: rs2201369; hg19: chr8-104222025;