dbSNP rs136002: ATXN10:c.1174-13649G>A (chr22-45793310-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_013236.4(ATXN10):c.1174-13649G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 171,808 control chromosomes in the GnomAD database, including 62,791 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 0.86 ( 56015 hom., cov: 32)

Exomes 𝑓: 0.83 ( 6776 hom. )

Consequence

ATXN10
NM_013236.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.01

Publications

5 publications found

Variant links:

Genes affected

ATXN10 (HGNC:10549): (ataxin 10) This gene encodes a protein that may function in neuron survival, neuron differentiation, and neuritogenesis. These roles may be carried out via activation of the mitogen-activated protein kinase cascade. Expansion of an ATTCT repeat from 9-32 copies to 800-4500 copies in an intronic region of this locus has been associated with spinocerebellar ataxia, type 10. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jul 2016]

ATXN10 links:

TRNT1P2 (HGNC:56782): (TRNT1 pseudogene 2)

TRNT1P2 links:

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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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013236.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATXN10	NM_013236.4	MANE Select	c.1174-13649G>A		intron	N/A	NP_037368.1	Q9UBB4-1
	ATXN10	NM_001167621.2		c.982-13649G>A		intron	N/A	NP_001161093.1	Q9UBB4-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ATXN10	ENST00000252934.10	TSL:1 MANE Select	c.1174-13649G>A	intron	N/A	ENSP00000252934.4	Q9UBB4-1
ATXN10	ENST00000381061.8	TSL:2	c.982-13649G>A	intron	N/A	ENSP00000370449.4	Q9UBB4-2
ATXN10	ENST00000435026.5	TSL:3	c.430-13649G>A	intron	N/A	ENSP00000391117.1	B1AHE4

Frequencies

GnomAD3 genomes

AF:

0.856

AC:

130206

AN:

152078

Hom.:

55953

Cov.:

show subpopulations

Gnomad AFR

AF:

0.931

Gnomad AMI

AF:

0.789

Gnomad AMR

AF:

0.861

Gnomad ASJ

AF:

0.850

Gnomad EAS

AF:

0.789

Gnomad SAS

AF:

0.845

Gnomad FIN

AF:

0.832

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.820

Gnomad OTH

AF:

0.864

GnomAD4 exome

AF:

0.831

AC:

16303

AN:

19612

Hom.:

6776

Cov.:

AF XY:

0.833

AC XY:

8277

AN XY:

9942

show subpopulations

African (AFR)

AF:

0.927

AC:

532

AN:

574

American (AMR)

AF:

0.811

AC:

532

AN:

656

Ashkenazi Jewish (ASJ)

AF:

0.844

AC:

559

AN:

662

East Asian (EAS)

AF:

0.697

AC:

619

AN:

888

South Asian (SAS)

AF:

0.829

AC:

378

AN:

456

European-Finnish (FIN)

AF:

0.932

AC:

1849

AN:

1984

Middle Eastern (MID)

AF:

0.875

AC:

1438

AN:

1644

European-Non Finnish (NFE)

AF:

0.813

AC:

9434

AN:

11606

Other (OTH)

AF:

0.842

AC:

962

AN:

1142

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

140

279

419

558

698

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

172

258

344

430

<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:

0.856

AC:

130326

AN:

152196

Hom.:

56015

Cov.:

AF XY:

0.857

AC XY:

63733

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.931

AC:

38691

AN:

41542

American (AMR)

AF:

0.861

AC:

13169

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.850

AC:

2948

AN:

3470

East Asian (EAS)

AF:

0.788

AC:

4079

AN:

5174

South Asian (SAS)

AF:

0.845

AC:

4068

AN:

4814

European-Finnish (FIN)

AF:

0.832

AC:

8807

AN:

10584

Middle Eastern (MID)

AF:

0.884

AC:

260

AN:

294

European-Non Finnish (NFE)

AF:

0.820

AC:

55758

AN:

68006

Other (OTH)

AF:

0.865

AC:

1826

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

973

1946

2918

3891

4864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<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:

0.824

Hom.:

25038

Bravo

AF:

0.862

Asia WGS

AF:

0.835

AC:

2904

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.53

(source)

DANN

Benign

0.32

PhyloP100

2.0

PromoterAI

-0.0062

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over