rs7026988

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000372348.9(ABL1):​c.137-61552C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,734 control chromosomes in the GnomAD database, including 4,859 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 0.22 ( 4859 hom., cov: 31)

Consequence

ABL1
ENST00000372348.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.187
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124902288XR_007061823.1 linkuse as main transcriptn.247-9718G>A intron_variant, non_coding_transcript_variant
ABL1NM_007313.3 linkuse as main transcriptc.137-61552C>T intron_variant
LOC124902288XR_007061824.1 linkuse as main transcriptn.247-4832G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ABL1ENST00000372348.9 linkuse as main transcriptc.137-61552C>T intron_variant 1 P1P00519-2
ABL1ENST00000393293.4 linkuse as main transcriptc.137-61555C>T intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.218
AC:
33121
AN:
151616
Hom.:
4855
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.428
Gnomad AMI
AF:
0.213
Gnomad AMR
AF:
0.200
Gnomad ASJ
AF:
0.120
Gnomad EAS
AF:
0.0682
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.118
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.135
Gnomad OTH
AF:
0.213
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33156
AN:
151734
Hom.:
4859
Cov.:
31
AF XY:
0.215
AC XY:
15913
AN XY:
74156
show subpopulations
Gnomad4 AFR
AF:
0.428
Gnomad4 AMR
AF:
0.200
Gnomad4 ASJ
AF:
0.120
Gnomad4 EAS
AF:
0.0682
Gnomad4 SAS
AF:
0.128
Gnomad4 FIN
AF:
0.118
Gnomad4 NFE
AF:
0.135
Gnomad4 OTH
AF:
0.212
Alfa
AF:
0.145
Hom.:
3849
Bravo
AF:
0.234
Asia WGS
AF:
0.127
AC:
440
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
8.1
DANN
Benign
0.73
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7026988; hg19: chr9-133667899; COSMIC: COSV64899641; API