Variant chr9-108972840-ATG-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003798.4(CTNNAL1):c.1189-9_1189-8delCA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 436,548 control chromosomes in the GnomAD database, including 271 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.034 ( 142 hom., cov: 18)

Exomes 𝑓: 0.0084 ( 129 hom. )

Consequence

CTNNAL1
NM_003798.4 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.71

Variant links:

Genes affected

CTNNAL1 (HGNC:2512): (catenin alpha like 1) Predicted to enable actin filament binding activity and cadherin binding activity. Acts upstream of or within Rho protein signal transduction. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

CTNNAL1 links:

CTNNAL1 (HGNC:):

CTNNAL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 9-108972840-ATG-A is Benign according to our data. Variant chr9-108972840-ATG-A is described in ClinVar as [Benign]. Clinvar id is 780822.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTNNAL1	NM_003798.4 linkuse as main transcript	c.1189-9_1189-8delCA		splice_region_variant, intron_variant		ENST00000325551.9	NP_003789.1	Q9UBT7-1B3KMX6

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
CTNNAL1	ENST00000325551.9 linkuse as main transcript	c.1189-9_1189-8delCA	splice_region_variant, intron_variant	1	NM_003798.4	ENSP00000320434.4	Q9UBT7-1
CTNNAL1	ENST00000374595.8 linkuse as main transcript	c.1189-9_1189-8delCA	splice_region_variant, intron_variant	1		ENSP00000363723.4	Q9UBT7-2
CTNNAL1	ENST00000488130.1 linkuse as main transcript	n.460-9_460-8delCA	splice_region_variant, intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.0344

AC:

3295

AN:

95740

Hom.:

143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0173

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000413

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0294

Gnomad NFE

AF:

0.000134

Gnomad OTH

AF:

0.0260

GnomAD3 exomes

AF:

0.00547

AC:

880

AN:

160922

Hom.:

AF XY:

0.00387

AC XY:

342

AN XY:

88486

show subpopulations

Gnomad AFR exome

AF:

0.0781

Gnomad AMR exome

AF:

0.00208

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000599

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000497

Gnomad OTH exome

AF:

0.00191

GnomAD4 exome

AF:

0.00840

AC:

2864

AN:

340772

Hom.:

129

AF XY:

0.00709

AC XY:

1288

AN XY:

181714

show subpopulations

Gnomad4 AFR exome

AF:

0.225

Gnomad4 AMR exome

AF:

0.00387

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000237

Gnomad4 SAS exome

AF:

0.000171

Gnomad4 FIN exome

AF:

0.0000586

Gnomad4 NFE exome

AF:

0.000212

Gnomad4 OTH exome

AF:

0.0179

GnomAD4 genome

AF:

0.0345

AC:

3301

AN:

95776

Hom.:

142

Cov.:

AF XY:

0.0361

AC XY:

1547

AN XY:

42866

show subpopulations

Gnomad4 AFR

AF:

0.126

Gnomad4 AMR

AF:

0.0173

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000134

Gnomad4 OTH

AF:

0.0258

Alfa

AF:

0.0156

Hom.:

Bravo

AF:

0.0297

Asia WGS

AF:

0.00607

AC:

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over