rs2201369

Positions:

• chr8-103209797-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BAALC	NM_024812.3	c.161-3122T>C		intron_variant		ENST00000309982.10
BAALC	NM_001024372.2	c.161-18192T>C		intron_variant
BAALC	NM_001364874.1	c.266-3122T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAALC	ENST00000309982.10	c.161-3122T>C		intron_variant		1	NM_024812.3	P1
BAALC-AS1	ENST00000499522.6	n.985+24483A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0667

Gnomad4 AMR AF: 0.0950

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0708

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.137

Alfa AF: 0.174 Hom.: 3288

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

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

LitVar

Other links and lift over

dbSNP: rs2201369; hg19: chr8-104222025;