Variant 11-2302811-A-G details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.59

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]

TSPAN32 links:

C11orf21 (HGNC:13231): (chromosome 11 open reading frame 21) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

C11orf21 links:

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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 (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	Protein	UniProt
TSPAN32	NM_139022.3 linkuse as main transcript	c.67-33A>G		intron_variant		ENST00000182290.9	NP_620591.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSPAN32	ENST00000182290.9 linkuse as main transcript	c.67-33A>G		intron_variant		1	NM_139022.3	ENSP00000182290	P2	Q96QS1-1

Frequencies

GnomAD3 genomes

AF:

0.897

AC:

136367

AN:

152070

Hom.:

61973

Cov.:

show subpopulations

Gnomad AFR

AF:

0.953

Gnomad AMI

AF:

0.929

Gnomad AMR

AF:

0.811

Gnomad ASJ

AF:

0.879

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.869

Gnomad FIN

AF:

0.831

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.931

Gnomad OTH

AF:

0.897

GnomAD3 exomes

AF:

0.854

AC:

206535

AN:

241866

Hom.:

90515

AF XY:

0.860

AC XY:

112973

AN XY:

131332

show subpopulations

Gnomad AFR exome

AF:

0.955

Gnomad AMR exome

AF:

0.785

Gnomad ASJ exome

AF:

0.878

Gnomad EAS exome

AF:

0.413

Gnomad SAS exome

AF:

0.870

Gnomad FIN exome

AF:

0.838

Gnomad NFE exome

AF:

0.929

Gnomad OTH exome

AF:

0.884

GnomAD4 exome

AF:

0.904

AC:

1296923

AN:

1434560

Hom.:

591975

Cov.:

AF XY:

0.903

AC XY:

645689

AN XY:

714706

show subpopulations

Gnomad4 AFR exome

AF:

0.957

Gnomad4 AMR exome

AF:

0.791

Gnomad4 ASJ exome

AF:

0.880

Gnomad4 EAS exome

AF:

0.432

Gnomad4 SAS exome

AF:

0.866

Gnomad4 FIN exome

AF:

0.839

Gnomad4 NFE exome

AF:

0.932

Gnomad4 OTH exome

AF:

0.883

GnomAD4 genome

AF:

0.897

AC:

136475

AN:

152188

Hom.:

62022

Cov.:

AF XY:

0.887

AC XY:

66010

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.953

Gnomad4 AMR

AF:

0.810

Gnomad4 ASJ

AF:

0.879

Gnomad4 EAS

AF:

0.423

Gnomad4 SAS

AF:

0.869

Gnomad4 FIN

AF:

0.831

Gnomad4 NFE

AF:

0.931

Gnomad4 OTH

AF:

0.896

Alfa

AF:

0.924

Hom.:

85815

Bravo

AF:

0.898

TwinsUK

AF:

0.938

AC:

3479

ALSPAC

AF:

0.927

AC:

3572

ESP6500AA

AF:

0.958

AC:

4218

ESP6500EA

AF:

0.927

AC:

7970

ExAC

AF:

0.862

AC:

104364

Asia WGS

AF:

0.741

AC:

2580

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.67

CADD

Benign

0.17

DANN

Benign

0.40

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0086

LIST_S2

Uncertain

0.90

MetaRNN

Benign

0.0000020

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.90

P;P;P

PROVEAN

Benign

-0.080

REVEL

Benign

0.0060

Sift

Pathogenic

0.0

Vest4

0.019

ClinPred

0.014

GERP RS

-5.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over