9-130738178-C-T

Variant summary

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

The ENST00000372348.9(ABL1):c.136+23723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 151,948 control chromosomes in the GnomAD database, including 3,440 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 0.19 (3440 hom., cov: 31)
• Consequence: ABL1 ENST00000372348.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

Genes affected

ABL1 (HGNC:76): (ABL proto-oncogene 1, non-receptor tyrosine kinase) This gene is a protooncogene that encodes a protein tyrosine kinase involved in a variety of cellular processes, including cell division, adhesion, differentiation, and response to stress. The activity of the protein is negatively regulated by its SH3 domain, whereby deletion of the region encoding this domain results in an oncogene. The ubiquitously expressed protein has DNA-binding activity that is regulated by CDC2-mediated phosphorylation, suggesting a cell cycle function. This gene has been found fused to a variety of translocation partner genes in various leukemias, most notably the t(9;22) translocation that results in a fusion with the 5' end of the breakpoint cluster region gene (BCR; MIM:151410). Alternative splicing of this gene results in two transcript variants, which contain alternative first exons that are spliced to the remaining common exons. [provided by RefSeq, Aug 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABL1	NM_007313.3	c.136+23723C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABL1	ENST00000372348.9	c.136+23723C>T		intron_variant		1		P1
ABL1	ENST00000393293.4	c.136+23723C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28700 AN: 151830 Hom.: 3443 Cov.: 31

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.0915

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.189 AC: 28689 AN: 151948 Hom.: 3440 Cov.: 31 AF XY: 0.186 AC XY: 13848 AN XY: 74256

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.0917

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.236

Alfa AF: 0.167 Hom.: 648

Bravo AF: 0.186

Asia WGS AF: 0.147 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.33

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: rs2583845; hg19: chr9-133613565; COSMIC: COSV64897151;