Variant 12-30982525-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001370302.1(TSPAN11):c.457-7C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00436 in 1,600,616 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0028 ( 0 hom., cov: 34)

Exomes 𝑓: 0.0045 ( 27 hom. )

Consequence

TSPAN11
NM_001370302.1 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.001596

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.635

Variant links:

Genes affected

TSPAN11 (HGNC:30795): (tetraspanin 11) Predicted to be involved in cell migration. Predicted to be integral component of membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TSPAN11 links:

TSPAN11-AS1 (HGNC:56687): (TSPAN11 antisense RNA 1)

TSPAN11-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 12-30982525-C-A is Benign according to our data. Variant chr12-30982525-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2642815.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 27 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSPAN11	NM_001370302.1 linkuse as main transcript	c.457-7C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000546076.6	NP_001357231.1
TSPAN11-AS1	XR_007063261.1 linkuse as main transcript	n.295-3850G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
TSPAN11	ENST00000546076.6 linkuse as main transcript	c.457-7C>A	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	2	NM_001370302.1	ENSP00000437403	P1
TSPAN11	ENST00000261177.10 linkuse as main transcript	c.457-7C>A	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000261177	P1
TSPAN11-AS1	ENST00000613860.4 linkuse as main transcript	n.508-3850G>T	intron_variant, non_coding_transcript_variant	5
TSPAN11	ENST00000535215.5 linkuse as main transcript	c.244-7C>A	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	2		ENSP00000445503

Frequencies

GnomAD3 genomes

AF:

0.00284

AC:

432

AN:

152264

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000651

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00144

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00376

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00470

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.00284

AC:

708

AN:

248876

Hom.:

AF XY:

0.00301

AC XY:

405

AN XY:

134700

show subpopulations

Gnomad AFR exome

AF:

0.000810

Gnomad AMR exome

AF:

0.00105

Gnomad ASJ exome

AF:

0.00171

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00278

Gnomad FIN exome

AF:

0.00344

Gnomad NFE exome

AF:

0.00417

Gnomad OTH exome

AF:

0.00231

GnomAD4 exome

AF:

0.00452

AC:

6551

AN:

1448234

Hom.:

Cov.:

AF XY:

0.00456

AC XY:

3274

AN XY:

717512

show subpopulations

Gnomad4 AFR exome

AF:

0.000451

Gnomad4 AMR exome

AF:

0.00117

Gnomad4 ASJ exome

AF:

0.00185

Gnomad4 EAS exome

AF:

0.0000255

Gnomad4 SAS exome

AF:

0.00253

Gnomad4 FIN exome

AF:

0.00449

Gnomad4 NFE exome

AF:

0.00518

Gnomad4 OTH exome

AF:

0.00449

GnomAD4 genome

AF:

0.00283

AC:

431

AN:

152382

Hom.:

Cov.:

AF XY:

0.00248

AC XY:

185

AN XY:

74516

show subpopulations

Gnomad4 AFR

AF:

0.000649

Gnomad4 AMR

AF:

0.00144

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00376

Gnomad4 NFE

AF:

0.00470

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.00316

Hom.:

Bravo

AF:

0.00240

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00398

EpiControl

AF:

0.00397

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

TSPAN11: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.77

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0016

dbscSNV1_RF

Benign

0.046

SpliceAI score (max)

0.16

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over