rs111340708

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000341259.7(SH2B3):​c.1236+4_1236+18delTGGGGTGGGGTGGGG variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000221 in 587,712 control chromosomes in the GnomAD database, including 1 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000034 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000020 ( 1 hom. )

Consequence

SH2B3
ENST00000341259.7 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.00
Variant links:
Genes affected
SH2B3 (HGNC:29605): (SH2B adaptor protein 3) This gene encodes a member of the SH2B adaptor family of proteins, which are involved in a range of signaling activities by growth factor and cytokine receptors. The encoded protein is a key negative regulator of cytokine signaling and plays a critical role in hematopoiesis. Mutations in this gene have been associated with susceptibility to celiac disease type 13 and susceptibility to insulin-dependent diabetes mellitus. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2014]
ATXN2 (HGNC:10555): (ataxin 2) This gene belongs to a group of genes that is associated with microsatellite-expansion diseases, a class of neurological and neuromuscular disorders caused by expansion of short stretches of repetitive DNA. The protein encoded by this gene has two globular domains near the N-terminus, one of which contains a clathrin-mediated trans-Golgi signal and an endoplasmic reticulum exit signal. The encoded cytoplasmic protein localizes to the endoplasmic reticulum and plasma membrane, is involved in endocytosis, and modulates mTOR signals, modifying ribosomal translation and mitochondrial function. The N-terminal region of the protein contains a polyglutamine tract of 14-31 residues that can be expanded in the pathogenic state to 32-200 residues. Intermediate length expansions of this tract increase susceptibility to amyotrophic lateral sclerosis, while long expansions of this tract result in spinocerebellar ataxia-2, an autosomal-dominantly inherited, neurodegenerative disorder. Genome-wide association studies indicate that loss-of-function mutations in this gene may be associated with susceptibility to type I diabetes, obesity and hypertension. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SH2B3NM_005475.3 linkc.1236+14_1236+28delTGGGGTGGGGTGGGG intron_variant Intron 6 of 7 ENST00000341259.7 NP_005466.1 Q9UQQ2Q59H48

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SH2B3ENST00000341259.7 linkc.1236+4_1236+18delTGGGGTGGGGTGGGG splice_region_variant, intron_variant Intron 6 of 7 1 NM_005475.3 ENSP00000345492.2 Q9UQQ2
SH2B3ENST00000538307.1 linkc.630+4_630+18delTGGGGTGGGGTGGGG splice_region_variant, intron_variant Intron 5 of 6 2 ENSP00000440597.1 F5GYM4
ATXN2ENST00000642389.2 linkn.*171-3375_*171-3361delCCCCACCCCACCCCA intron_variant Intron 26 of 26 ENSP00000496055.2 A0A2R8Y7E6

Frequencies

GnomAD3 genomes
AF:
0.0000335
AC:
3
AN:
89446
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000823
Gnomad OTH
AF:
0.00
GnomAD2 exomes
AF:
0.0000162
AC:
3
AN:
184788
AF XY:
0.00000965
show subpopulations
Gnomad AFR exome
AF:
0.0000794
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000235
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000201
AC:
10
AN:
498266
Hom.:
1
AF XY:
0.0000191
AC XY:
5
AN XY:
261132
show subpopulations
African (AFR)
AF:
0.0000511
AC:
1
AN:
19554
American (AMR)
AF:
0.00
AC:
0
AN:
26140
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
9094
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35508
South Asian (SAS)
AF:
0.00
AC:
0
AN:
53320
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
28470
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3422
European-Non Finnish (NFE)
AF:
0.0000201
AC:
6
AN:
299036
Other (OTH)
AF:
0.000126
AC:
3
AN:
23722
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.600
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

Exome Het
Exome Hom
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
GnomAD4 genome
AF:
0.0000335
AC:
3
AN:
89446
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
42374
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
30892
American (AMR)
AF:
0.00
AC:
0
AN:
8304
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
1608
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4278
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2724
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
3384
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
200
European-Non Finnish (NFE)
AF:
0.0000823
AC:
3
AN:
36436
Other (OTH)
AF:
0.00
AC:
0
AN:
1212
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
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
Alfa
AF:
0.00
Hom.:
272

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs111340708; hg19: chr12-111885351; API