Variant rs8668 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

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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=-0.82).

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/exons	MANE	Protein	UniProt
CABLES2	NM_031215.3 linkuse as main transcript	c.*1963T>C		3_prime_UTR_variant	10/10	ENST00000279101.10	NP_112492.2
CABLES2	XM_047440530.1 linkuse as main transcript	c.*1963T>C		3_prime_UTR_variant	8/8		XP_047296486.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CABLES2	ENST00000279101.10 linkuse as main transcript	c.*1963T>C		3_prime_UTR_variant	10/10	5	NM_031215.3	ENSP00000279101	P1

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

Gnomad4 AFR exome

AF:

0.367

Gnomad4 AMR exome

AF:

0.311

Gnomad4 ASJ exome

AF:

0.412

Gnomad4 EAS exome

AF:

0.123

Gnomad4 SAS exome

AF:

0.313

Gnomad4 FIN exome

AF:

0.222

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.298

GnomAD4 genome

AF:

0.329

AC:

50026

AN:

152242

Hom.:

8887

Cov.:

AF XY:

0.324

AC XY:

24084

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.446

Gnomad4 AMR

AF:

0.329

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.141

Gnomad4 SAS

AF:

0.256

Gnomad4 FIN

AF:

0.234

Gnomad4 NFE

AF:

0.292

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.306

Hom.:

9257

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

DANN

Benign

0.40

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over