rs1325195

Variant names:

• chr1-179102621-G-A
• rs1325195
• NM_007314.4:c.*5097C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-179102621-G-A
• chr1-179102621-G-C
• chr1-179102621-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007314.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABL2	NM_007314.4	MANE Select	c.*5097C>T		3_prime_UTR	Exon 12 of 12	NP_009298.1
	ABL2	NM_005158.5		c.*5097C>T		3_prime_UTR	Exon 12 of 12	NP_005149.4
	ABL2	NM_001168236.2		c.*5097C>T		3_prime_UTR	Exon 11 of 11	NP_001161708.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABL2	ENST00000502732.6	TSL:1 MANE Select	c.*5097C>T		3_prime_UTR	Exon 12 of 12	ENSP00000427562.1
	ABL2	ENST00000344730.8	TSL:1	c.*5097C>T		3_prime_UTR	Exon 13 of 13	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

African (AFR) AF: 0.680 AC: 2455 AN: 3608

American (AMR) AF: 0.520 AC: 1210 AN: 2326

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 3313 AN: 4762

East Asian (EAS) AF: 0.568 AC: 6128 AN: 10786

South Asian (SAS) AF: 0.630 AC: 416 AN: 660

European-Finnish (FIN) AF: 0.648 AC: 35 AN: 54

Middle Eastern (MID) AF: 0.629 AC: 283 AN: 450

European-Non Finnish (NFE) AF: 0.595 AC: 27919 AN: 46910

Other (OTH) AF: 0.623 AC: 3970 AN: 6374

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

African (AFR) AF: 0.674 AC: 27914 AN: 41442

American (AMR) AF: 0.547 AC: 8364 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2428 AN: 3472

East Asian (EAS) AF: 0.514 AC: 2648 AN: 5148

South Asian (SAS) AF: 0.660 AC: 3182 AN: 4822

European-Finnish (FIN) AF: 0.604 AC: 6381 AN: 10558

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40798 AN: 67980

Other (OTH) AF: 0.630 AC: 1330 AN: 2112

Alfa AF: 0.606 Hom.: 44887

Bravo AF: 0.611

Asia WGS AF: 0.622 AC: 2166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.69
PhyloP100		0.95
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1325195; hg19: chr1-179071756;