Variant chrX-13318985-CTTG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2

The NM_001135995.2(ATXN3L):c.947_949delCAA(p.Thr316del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000643 in 1,210,201 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 251 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00036 ( 0 hom., 9 hem., cov: 23)

Exomes 𝑓: 0.00067 ( 0 hom. 242 hem. )

Consequence

ATXN3L
NM_001135995.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.718

Variant links:

Genes affected

ATXN3L (HGNC:24173): (ataxin 3 like) This intronless gene may be a pseudogene (PMID:11450850). This gene is similar to the multi-exon gene which encodes ataxin 3 and contains a coding region which could encode a protein similar to ataxin 3. Mutations in the gene encoding ataxin 3 are associated with Machado-Joseph disease. [provided by RefSeq, Sep 2011]

ATXN3L links:

GS1-600G8.3 (HGNC:):

GS1-600G8.3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001135995.2. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant X-13318985-CTTG-C is Benign according to our data. Variant chrX-13318985-CTTG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2660021.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATXN3L	NM_001135995.2 linkuse as main transcript	c.947_949delCAA	p.Thr316del	disruptive_inframe_deletion	1/1	ENST00000380622.5	NP_001129467.1	Q9H3M9B4DYC7
ATXN3L	NM_001387036.1 linkuse as main transcript	c.683_685delCAA	p.Thr228del	disruptive_inframe_deletion	2/2		NP_001373965.1
GS1-600G8.3	NR_046087.1 linkuse as main transcript	n.1449-16_1449-14delTTG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATXN3L	ENST00000380622.5 linkuse as main transcript	c.947_949delCAA	p.Thr316del	disruptive_inframe_deletion	1/1	6	NM_001135995.2	ENSP00000369996.2		Q9H3M9
GS1-600G8.3	ENST00000431486.1 linkuse as main transcript	n.1449-16_1449-14delTTG		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.000357

AC:

AN:

112185

Hom.:

Cov.:

AF XY:

0.000233

AC XY:

AN XY:

34337

show subpopulations

Gnomad AFR

AF:

0.000130

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000552

Gnomad SAS

AF:

0.000746

Gnomad FIN

AF:

0.000165

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000563

Gnomad OTH

AF:

0.000664

GnomAD3 exomes

AF:

0.000536

AC:

AN:

181061

Hom.:

AF XY:

0.000548

AC XY:

AN XY:

67477

show subpopulations

Gnomad AFR exome

AF:

0.0000810

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00118

Gnomad SAS exome

AF:

0.000944

Gnomad FIN exome

AF:

0.000314

Gnomad NFE exome

AF:

0.000667

Gnomad OTH exome

AF:

0.000673

GnomAD4 exome

AF:

0.000672

AC:

738

AN:

1097962

Hom.:

AF XY:

0.000666

AC XY:

242

AN XY:

363390

show subpopulations

Gnomad4 AFR exome

AF:

0.000114

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000364

Gnomad4 SAS exome

AF:

0.000997

Gnomad4 FIN exome

AF:

0.0000987

Gnomad4 NFE exome

AF:

0.000735

Gnomad4 OTH exome

AF:

0.00102

GnomAD4 genome

AF:

0.000356

AC:

AN:

112239

Hom.:

Cov.:

AF XY:

0.000262

AC XY:

AN XY:

34401

show subpopulations

Gnomad4 AFR

AF:

0.000129

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000554

Gnomad4 SAS

AF:

0.000748

Gnomad4 FIN

AF:

0.000165

Gnomad4 NFE

AF:

0.000563

Gnomad4 OTH

AF:

0.000655

Alfa

AF:

0.000738

Hom.:

Bravo

AF:

0.000348

Asia WGS

AF:

0.000398

AC:

AN:

2522

EpiCase

AF:

0.000654

EpiControl

AF:

0.000652

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

ATXN3L: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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