rs2074022
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_139022.3(TSPAN32):c.67-33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 1,586,748 control chromosomes in the GnomAD database, including 653,997 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 0.90 ( 62022 hom., cov: 32)
Exomes 𝑓: 0.90 ( 591975 hom. )
Consequence
TSPAN32
NM_139022.3 intron
NM_139022.3 intron
Scores
1
1
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.59
Genes affected
TSPAN32 (HGNC:13410): (tetraspanin 32) This gene, which is a member of the tetraspanin superfamily, is one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of chromosome 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian and breast cancers. This gene is located among several imprinted genes; however, this gene, as well as the tumor-suppressing subchromosomal transferable fragment 4, escapes imprinting. This gene may play a role in malignancies and diseases that involve this region, and it is also involved in hematopoietic cell function. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=1.9928798E-6).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPAN32 | NM_139022.3 | c.67-33A>G | intron_variant | ENST00000182290.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPAN32 | ENST00000182290.9 | c.67-33A>G | intron_variant | 1 | NM_139022.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.897 AC: 136367AN: 152070Hom.: 61973 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
136367
AN:
152070
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.854 AC: 206535AN: 241866Hom.: 90515 AF XY: 0.860 AC XY: 112973AN XY: 131332
GnomAD3 exomes
AF:
AC:
206535
AN:
241866
Hom.:
AF XY:
AC XY:
112973
AN XY:
131332
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.904 AC: 1296923AN: 1434560Hom.: 591975 Cov.: 24 AF XY: 0.903 AC XY: 645689AN XY: 714706
GnomAD4 exome
AF:
AC:
1296923
AN:
1434560
Hom.:
Cov.:
24
AF XY:
AC XY:
645689
AN XY:
714706
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.897 AC: 136475AN: 152188Hom.: 62022 Cov.: 32 AF XY: 0.887 AC XY: 66010AN XY: 74382
GnomAD4 genome
?
AF:
AC:
136475
AN:
152188
Hom.:
Cov.:
32
AF XY:
AC XY:
66010
AN XY:
74382
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
3479
ALSPAC
AF:
AC:
3572
ESP6500AA
AF:
AC:
4218
ESP6500EA
AF:
AC:
7970
ExAC
?
AF:
AC:
104364
Asia WGS
AF:
AC:
2580
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Vest4
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at