chr1-179102621-G-A

Position:

• chr1-179102621-G-A

Variant summary

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

The NM_007314.4(ABL2):​c.*5097C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 227,946 control chromosomes in the GnomAD database, including 43,080 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 0.62 (29130 hom., cov: 31)
  • Exomes 𝑓: 0.60 (13950 hom.)
• Consequence: ABL2 NM_007314.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951

Genes affected

ABL2 (HGNC:77): (ABL proto-oncogene 2, non-receptor tyrosine kinase) This gene encodes a member of the Abelson family of nonreceptor tyrosine protein kinases. The protein is highly similar to the c-abl oncogene 1 protein, including the tyrosine kinase, SH2 and SH3 domains, and it plays a role in cytoskeletal rearrangements through its C-terminal F-actin- and microtubule-binding sequences. This gene is expressed in both normal and tumor cells, and is involved in translocation with the ets variant 6 gene in leukemia. Multiple alternatively spliced transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABL2	NM_007314.4	c.*5097C>T		3_prime_UTR_variant	12/12	ENST00000502732.6	NP_009298.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABL2	ENST00000502732	c.*5097C>T		3_prime_UTR_variant	12/12	1	NM_007314.4	ENSP00000427562.1
ABL2	ENST00000344730	c.*5097C>T		3_prime_UTR_variant	13/13	1		ENSP00000339209.3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93578 AN: 151898 Hom.: 29085 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.626

GnomAD4 exome AF: 0.602 AC: 45729 AN: 75930 Hom.: 13950 Cov.: 0 AF XY: 0.605 AC XY: 21104 AN XY: 34884

Gnomad4 AFR exome AF: 0.680

Gnomad4 AMR exome AF: 0.520

Gnomad4 ASJ exome AF: 0.696

Gnomad4 EAS exome AF: 0.568

Gnomad4 SAS exome AF: 0.630

Gnomad4 FIN exome AF: 0.648

Gnomad4 NFE exome AF: 0.595

Gnomad4 OTH exome AF: 0.623

GnomAD4 genome AF: 0.616 AC: 93674 AN: 152016 Hom.: 29130 Cov.: 31 AF XY: 0.618 AC XY: 45883 AN XY: 74290

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.630

Alfa AF: 0.602 Hom.: 26908

Bravo AF: 0.611

Asia WGS AF: 0.622 AC: 2166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.69

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: rs1325195; hg19: chr1-179071756;