Genetic Variant TAPBPL:c.1208-38C>T (chr12-6460817-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018009.5(TAPBPL):c.1208-38C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 1,604,406 control chromosomes in the GnomAD database, including 68,157 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 0.24 ( 5025 hom., cov: 32)

Exomes 𝑓: 0.29 ( 63132 hom. )

Consequence

TAPBPL
NM_018009.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00100

Publications

22 publications found

Variant links:

Genes affected

TAPBPL (HGNC:30683): (TAP binding protein like) Tapasin, or TAPBP (MIM 601962), is a member of the variable-constant Ig superfamily that links major histocompatibility complex (MHC) class I molecules to the transporter associated with antigen processing (TAP; see MIM 170260) in the endoplasmic reticulum (ER). The TAPBP gene is located near the MHC complex on chromosome 6p21.3. TAPBPL is a member of the Ig superfamily that is localized on chromosome 12p13.3, a region somewhat paralogous to the MHC.[supplied by OMIM, Mar 2008]

TAPBPL links:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAPBPL	NM_018009.5 link	c.1208-38C>T		intron_variant	Intron 5 of 6	ENST00000266556.8	NP_060479.3	Q9BX59-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAPBPL	ENST00000266556.8 link	c.1208-38C>T		intron_variant	Intron 5 of 6	1	NM_018009.5	ENSP00000266556.7		Q9BX59-1

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36893

AN:

152006

Hom.:

5025

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.420

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.325

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.248

GnomAD2 exomes

AF:

0.273

AC:

68205

AN:

249896

AF XY:

0.284

show subpopulations

Gnomad AFR exome

AF:

0.110

Gnomad AMR exome

AF:

0.146

Gnomad ASJ exome

AF:

0.293

Gnomad EAS exome

AF:

0.345

Gnomad FIN exome

AF:

0.297

Gnomad NFE exome

AF:

0.299

Gnomad OTH exome

AF:

0.281

GnomAD4 exome

AF:

0.292

AC:

423452

AN:

1452282

Hom.:

63132

Cov.:

AF XY:

0.295

AC XY:

212994

AN XY:

723034

show subpopulations

African (AFR)

AF:

0.109

AC:

3632

AN:

33280

American (AMR)

AF:

0.152

AC:

6791

AN:

44644

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

7479

AN:

26040

East Asian (EAS)

AF:

0.345

AC:

13667

AN:

39612

South Asian (SAS)

AF:

0.342

AC:

29447

AN:

86010

European-Finnish (FIN)

AF:

0.294

AC:

15678

AN:

53250

Middle Eastern (MID)

AF:

0.319

AC:

1831

AN:

5744

European-Non Finnish (NFE)

AF:

0.297

AC:

327868

AN:

1103674

Other (OTH)

AF:

0.284

AC:

17059

AN:

60028

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

15063

30126

45188

60251

75314

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10690

21380

32070

42760

53450

<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:

0.243

AC:

36902

AN:

152124

Hom.:

5025

Cov.:

AF XY:

0.244

AC XY:

18148

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.117

AC:

4854

AN:

41516

American (AMR)

AF:

0.222

AC:

3392

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.286

AC:

991

AN:

3470

East Asian (EAS)

AF:

0.331

AC:

1715

AN:

5176

South Asian (SAS)

AF:

0.348

AC:

1679

AN:

4822

European-Finnish (FIN)

AF:

0.301

AC:

3185

AN:

10572

Middle Eastern (MID)

AF:

0.342

AC:

100

AN:

292

European-Non Finnish (NFE)

AF:

0.295

AC:

20073

AN:

67962

Other (OTH)

AF:

0.251

AC:

530

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1402

2804

4207

5609

7011

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.257

Hom.:

2558

Bravo

AF:

0.227

Asia WGS

AF:

0.253

AC:

881

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.1

(source)

DANN

Benign

0.48

PhyloP100

0.0010

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over