Genetic Variant TSPAN11:c.*3337G>A (chr12-30995252-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001370302.1(TSPAN11):c.*3337G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,370 control chromosomes in the GnomAD database, including 1,554 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 0.13 ( 1554 hom., cov: 33)

Exomes 𝑓: 0.092 ( 0 hom. )

Consequence

TSPAN11
NM_001370302.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0890

Publications

4 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370302.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TSPAN11	NM_001370302.1	MANE Select	c.*3337G>A	3_prime_UTR	Exon 8 of 8	NP_001357231.1
TSPAN11	NM_001080509.3		c.*3337G>A	3_prime_UTR	Exon 8 of 8	NP_001073978.1
TSPAN11	NM_001370301.1		c.*3337G>A	3_prime_UTR	Exon 7 of 7	NP_001357230.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TSPAN11	ENST00000546076.6	TSL:2 MANE Select	c.*3337G>A	3_prime_UTR	Exon 8 of 8	ENSP00000437403.1
TSPAN11	ENST00000261177.10	TSL:1	c.*3337G>A	3_prime_UTR	Exon 8 of 8	ENSP00000261177.9
TSPAN11-AS1	ENST00000613860.4	TSL:5	n.401+735C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.132

AC:

20052

AN:

152130

Hom.:

1560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.246

Gnomad AMR

AF:

0.0953

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.0911

Gnomad MID

AF:

0.236

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.148

GnomAD4 exome

AF:

0.0917

AC:

AN:

120

Hom.:

Cov.:

AF XY:

0.0978

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0918

AC:

AN:

Other (OTH)

AF:

0.100

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.132

AC:

20035

AN:

152250

Hom.:

1554

Cov.:

AF XY:

0.132

AC XY:

9804

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.111

AC:

4611

AN:

41558

American (AMR)

AF:

0.0952

AC:

1456

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

428

AN:

3468

East Asian (EAS)

AF:

0.351

AC:

1810

AN:

5164

South Asian (SAS)

AF:

0.263

AC:

1264

AN:

4814

European-Finnish (FIN)

AF:

0.0911

AC:

968

AN:

10620

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.131

AC:

8897

AN:

68004

Other (OTH)

AF:

0.147

AC:

310

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

888

1777

2665

3554

4442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

240

480

720

960

1200

<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:

0.134

Hom.:

2752

Bravo

AF:

0.131

Asia WGS

AF:

0.301

AC:

1043

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.85

(source)

DANN

Benign

0.61

PhyloP100

-0.089

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over