rs800140

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_139022.3(TSPAN32):​c.355-1209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,208 control chromosomes in the GnomAD database, including 29,169 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 0.58 ( 29169 hom., cov: 35)

Consequence

TSPAN32
NM_139022.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TSPAN32NM_139022.3 linkuse as main transcriptc.355-1209A>G intron_variant ENST00000182290.9 NP_620591.3
LOC124902612XR_007062552.1 linkuse as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSPAN32ENST00000182290.9 linkuse as main transcriptc.355-1209A>G intron_variant 1 NM_139022.3 ENSP00000182290 P2Q96QS1-1

Frequencies

GnomAD3 genomes
AF:
0.577
AC:
87757
AN:
152090
Hom.:
29173
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.246
Gnomad AMI
AF:
0.855
Gnomad AMR
AF:
0.574
Gnomad ASJ
AF:
0.688
Gnomad EAS
AF:
0.384
Gnomad SAS
AF:
0.686
Gnomad FIN
AF:
0.647
Gnomad MID
AF:
0.601
Gnomad NFE
AF:
0.765
Gnomad OTH
AF:
0.616
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.577
AC:
87754
AN:
152208
Hom.:
29169
Cov.:
35
AF XY:
0.572
AC XY:
42568
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.245
Gnomad4 AMR
AF:
0.573
Gnomad4 ASJ
AF:
0.688
Gnomad4 EAS
AF:
0.383
Gnomad4 SAS
AF:
0.686
Gnomad4 FIN
AF:
0.647
Gnomad4 NFE
AF:
0.765
Gnomad4 OTH
AF:
0.616
Alfa
AF:
0.719
Hom.:
18467
Bravo
AF:
0.554
Asia WGS
AF:
0.554
AC:
1932
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.12
DANN
Benign
0.57

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs800140; hg19: chr11-2333675; API