rs6468862

chr8-103163348-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024812.3(BAALC):c.160+22291C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,902 control chromosomes in the GnomAD database, including 13,685 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 0.41 (13685 hom., cov: 31)
• Consequence: BAALC NM_024812.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAALC	NM_024812.3	c.160+22291C>T		intron_variant		ENST00000309982.10
BAALC-AS1	NR_109954.1	n.677+2477G>A		intron_variant, non_coding_transcript_variant
BAALC	NM_001024372.2	c.160+22291C>T		intron_variant
BAALC	NM_001364874.1	c.160+22291C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAALC	ENST00000309982.10	c.160+22291C>T		intron_variant		1	NM_024812.3	P1

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62842 AN: 151784 Hom.: 13676 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.414 AC: 62888 AN: 151902 Hom.: 13685 Cov.: 31 AF XY: 0.405 AC XY: 30065 AN XY: 74252

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.0323

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.412

Alfa AF: 0.454 Hom.: 22564

Bravo AF: 0.404

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.3
Dann	Benign	0.45

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: rs6468862; hg19: chr8-104175576;