Genetic Variant CABLES2:c.*1963T>C (chr20-62389008-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031215.3(CABLES2):c.*1963T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 157,602 control chromosomes in the GnomAD database, including 9,139 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 0.33 ( 8887 hom., cov: 35)

Exomes 𝑓: 0.30 ( 252 hom. )

Consequence

CABLES2
NM_031215.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750

Publications

18 publications found

Variant links:

Genes affected

CABLES2 (HGNC:16143): (Cdk5 and Abl enzyme substrate 2) Predicted to be involved in cell division and regulation of cell cycle. [provided by Alliance of Genome Resources, Apr 2022]

CABLES2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CABLES2	NM_031215.3 link	c.*1963T>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000279101.10	NP_112492.2	Q9BTV7
CABLES2	XM_047440530.1 link	c.*1963T>C		3_prime_UTR_variant	Exon 8 of 8		XP_047296486.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CABLES2	ENST00000279101.10 link	c.*1963T>C		3_prime_UTR_variant	Exon 10 of 10	5	NM_031215.3	ENSP00000279101.5		Q9BTV7

Frequencies

GnomAD3 genomes

AF:

0.329

AC:

49975

AN:

152124

Hom.:

8876

Cov.:

show subpopulations

Gnomad AFR

AF:

0.446

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.322

GnomAD4 exome

AF:

0.296

AC:

1589

AN:

5360

Hom.:

252

Cov.:

AF XY:

0.288

AC XY:

823

AN XY:

2856

show subpopulations

African (AFR)

AF:

0.367

AC:

AN:

American (AMR)

AF:

0.311

AC:

292

AN:

940

Ashkenazi Jewish (ASJ)

AF:

0.412

AC:

AN:

East Asian (EAS)

AF:

0.123

AC:

AN:

122

South Asian (SAS)

AF:

0.313

AC:

248

AN:

792

European-Finnish (FIN)

AF:

0.222

AC:

AN:

Middle Eastern (MID)

AF:

0.625

AC:

AN:

European-Non Finnish (NFE)

AF:

0.292

AC:

912

AN:

3120

Other (OTH)

AF:

0.298

AC:

AN:

208

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

116

174

232

290

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.329

AC:

50026

AN:

152242

Hom.:

8887

Cov.:

AF XY:

0.324

AC XY:

24084

AN XY:

74430

show subpopulations

African (AFR)

AF:

0.446

AC:

18529

AN:

41524

American (AMR)

AF:

0.329

AC:

5032

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.326

AC:

1133

AN:

3472

East Asian (EAS)

AF:

0.141

AC:

729

AN:

5186

South Asian (SAS)

AF:

0.256

AC:

1237

AN:

4830

European-Finnish (FIN)

AF:

0.234

AC:

2484

AN:

10604

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.292

AC:

19869

AN:

68008

Other (OTH)

AF:

0.318

AC:

673

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1769

3538

5308

7077

8846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.315

Hom.:

18538

Bravo

AF:

0.341

Asia WGS

AF:

0.207

AC:

720

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.6

(source)

DANN

Benign

0.40

PhyloP100

-0.075

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over