rs1554664711
Your query was ambiguous. Multiple possible variants found:
- chr9-32986032-T-TAAAAAAAAACA
- chr9-32986032-T-TAAAAAAAAACAA
- chr9-32986032-T-TAAAAAAAAACAAA
- chr9-32986032-T-TAAAAAAAAAC
- chr9-32986032-T-TAAAAAAAAACAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAA
- chr9-32986032-T-TAAAAAAAAACAAAAAAAAAAAACAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAACCAAAAAAAAAAAAAAAAA
- chr9-32986032-T-TAAAAAAAAATAAAAAA
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001195248.2(APTX):c.484-3_484-2insTGTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00028 ( 0 hom., cov: 0)
Exomes 𝑓: 0.00059 ( 3 hom. )
Consequence
APTX
NM_001195248.2 splice_region, intron
NM_001195248.2 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.384
Publications
0 publications found
Genes affected
APTX (HGNC:15984): (aprataxin) This gene encodes a member of the histidine triad (HIT) superfamily. The encoded protein may play a role in single-stranded DNA repair through its nucleotide-binding activity and its diadenosine polyphosphate hydrolase activity. Mutations in this gene have been associated with ataxia-ocular apraxia. Alternatively spliced transcript variants have been identified for this gene.[provided by RefSeq, Aug 2010]
APTX Gene-Disease associations (from GenCC):
- ataxia, early-onset, with oculomotor apraxia and hypoalbuminemiaInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet, Genomics England PanelApp
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 9-32986032-T-TAAAAAAAAACA is Benign according to our data. Variant chr9-32986032-T-TAAAAAAAAACA is described in ClinVar as Likely_benign. ClinVar VariationId is 2693722.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. GnomAdExome4 allele frequency = 0.000586 (421/718738) while in subpopulation EAS AF = 0.00196 (48/24444). AF 95% confidence interval is 0.00152. There are 3 homozygotes in GnomAdExome4. There are 224 alleles in the male GnomAdExome4 subpopulation. Median coverage is 10. This position passed quality control check.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001195248.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| APTX | MANE Select | c.484-3_484-2insTGTTTTTTTTT | splice_region intron | N/A | NP_001182177.2 | Q7Z2E3-7 | |||
| APTX | c.484-3_484-2insTGTTTTTTTTT | splice_region intron | N/A | NP_001182178.1 | Q7Z2E3-7 | ||||
| APTX | c.484-3_484-2insTGTTTTTTTTT | splice_region intron | N/A | NP_001355924.1 | Q7Z2E3-7 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| APTX | TSL:1 MANE Select | c.484-3_484-2insTGTTTTTTTTT | splice_region intron | N/A | ENSP00000369145.2 | Q7Z2E3-7 | |||
| APTX | TSL:1 | c.484-3_484-2insTGTTTTTTTTT | splice_region intron | N/A | ENSP00000369147.2 | Q7Z2E3-7 | |||
| APTX | TSL:1 | c.484-3_484-2insTGTTTTTTTTT | splice_region intron | N/A | ENSP00000419846.1 | Q7Z2E3-7 |
Frequencies
GnomAD3 genomes 0.000278 AC: 4AN: 14364Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
4
AN:
14364
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000586 AC: 421AN: 718738Hom.: 3 Cov.: 10 AF XY: 0.000603 AC XY: 224AN XY: 371534 show subpopulations
GnomAD4 exome
AF:
AC:
421
AN:
718738
Hom.:
Cov.:
10
AF XY:
AC XY:
224
AN XY:
371534
show subpopulations
African (AFR)
AF:
AC:
17
AN:
15456
American (AMR)
AF:
AC:
27
AN:
24798
Ashkenazi Jewish (ASJ)
AF:
AC:
7
AN:
16114
East Asian (EAS)
AF:
AC:
48
AN:
24444
South Asian (SAS)
AF:
AC:
83
AN:
51516
European-Finnish (FIN)
AF:
AC:
13
AN:
28438
Middle Eastern (MID)
AF:
AC:
1
AN:
2306
European-Non Finnish (NFE)
AF:
AC:
205
AN:
523876
Other (OTH)
AF:
AC:
20
AN:
31790
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.414
Heterozygous variant carriers
0
12
24
37
49
61
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
10
20
30
40
50
<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 0.000279 AC: 4AN: 14360Hom.: 0 Cov.: 0 AF XY: 0.000451 AC XY: 3AN XY: 6650 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
4
AN:
14360
Hom.:
Cov.:
0
AF XY:
AC XY:
3
AN XY:
6650
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
5168
American (AMR)
AF:
AC:
0
AN:
1182
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
320
East Asian (EAS)
AF:
AC:
0
AN:
464
South Asian (SAS)
AF:
AC:
1
AN:
384
European-Finnish (FIN)
AF:
AC:
0
AN:
556
Middle Eastern (MID)
AF:
AC:
0
AN:
42
European-Non Finnish (NFE)
AF:
AC:
2
AN:
6066
Other (OTH)
AF:
AC:
0
AN:
120
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000000000130562), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.263
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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