chr8-103141321-G-T

Variant names:

• chr8-103141321-G-T
• rs62527607
• NM_024812.3:c.160+264G>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+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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAALC	NM_024812.3	c.160+264G>T		intron_variant	Intron 1 of 2	ENST00000309982.10	NP_079088.1
BAALC	NM_001364874.1	c.160+264G>T		intron_variant	Intron 1 of 3		NP_001351803.1
BAALC	NM_001024372.2	c.160+264G>T		intron_variant	Intron 1 of 1		NP_001019543.1
BAALC-AS2	NR_027071.1	n.22C>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAALC	ENST00000309982.10	c.160+264G>T		intron_variant	Intron 1 of 2	1	NM_024812.3	ENSP00000312457.5

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20325 AN: 152024 Hom.: 1522 Cov.: 33

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.: 4 AF XY: 0.139 AC XY: 17597 AN XY: 126154

Gnomad4 AFR exome AF: 0.111

Gnomad4 AMR exome AF: 0.0927

Gnomad4 ASJ exome AF: 0.155

Gnomad4 EAS exome AF: 0.000102

Gnomad4 SAS exome AF: 0.0824

Gnomad4 FIN exome AF: 0.216

Gnomad4 NFE exome AF: 0.155

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.134 AC: 20339 AN: 152142 Hom.: 1520 Cov.: 33 AF XY: 0.133 AC XY: 9878 AN XY: 74358

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0995

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.000971

Gnomad4 SAS AF: 0.0785

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.133

Alfa AF: 0.142 Hom.: 205

Bravo AF: 0.124

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.055
DANN	Benign	0.78

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: rs62527607; hg19: chr8-104153549; COSMIC: COSV52564483;