rs241449

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001290043.2(TAP2):c.*30G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,524,222 control chromosomes in the GnomAD database, including 57,377 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5641 hom., cov: 31)

Exomes 𝑓: 0.27 ( 51736 hom. )

Consequence

TAP2
NM_001290043.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0730

Publications

45 publications found

Variant links:

Genes affected

TAP2 (HGNC:44): (transporter 2, ATP binding cassette subfamily B member) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. This gene is located 7 kb telomeric to gene family member ABCB2. The protein encoded by this gene is involved in antigen presentation. This protein forms a heterodimer with ABCB2 in order to transport peptides from the cytoplasm to the endoplasmic reticulum. Mutations in this gene may be associated with ankylosing spondylitis, insulin-dependent diabetes mellitus, and celiac disease. Alternative splicing of this gene produces products which differ in peptide selectivity and level of restoration of surface expression of MHC class I molecules. [provided by RefSeq, Feb 2014]

TAP2 Gene-Disease associations (from GenCC):

MHC class I deficiency
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen

TAP2 links:

ENSG00000250264 (HGNC:):

ENSG00000250264 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 6-32828876-C-A is Benign according to our data. Variant chr6-32828876-C-A is described in ClinVar as Benign. ClinVar VariationId is 403509.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAP2	NM_001290043.2 link	c.*30G>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000374897.4	NP_001276972.1	Q03519-1Q5JNW1
TAP2	NM_018833.3 link	c.1932+524G>T		intron_variant	Intron 11 of 11		NP_061313.2	Q03519-2Q9UP03

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAP2	ENST00000374897.4 link	c.*30G>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_001290043.2	ENSP00000364032.3		Q03519-1
ENSG00000250264	ENST00000452392.2 link	c.1932+524G>T		intron_variant	Intron 11 of 14	2		ENSP00000391806.2		E7ENX8

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40190

AN:

151888

Hom.:

5630

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.399

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.291

GnomAD2 exomes

AF:

0.314

AC:

46386

AN:

147522

AF XY:

0.316

show subpopulations

Gnomad AFR exome

AF:

0.177

Gnomad AMR exome

AF:

0.355

Gnomad ASJ exome

AF:

0.343

Gnomad EAS exome

AF:

0.362

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.299

GnomAD4 exome

AF:

0.269

AC:

368871

AN:

1372214

Hom.:

51736

Cov.:

AF XY:

0.272

AC XY:

182858

AN XY:

671772

show subpopulations

African (AFR)

AF:

0.184

AC:

5743

AN:

31232

American (AMR)

AF:

0.348

AC:

12332

AN:

35456

Ashkenazi Jewish (ASJ)

AF:

0.349

AC:

8700

AN:

24952

East Asian (EAS)

AF:

0.354

AC:

12421

AN:

35116

South Asian (SAS)

AF:

0.393

AC:

30510

AN:

77614

European-Finnish (FIN)

AF:

0.335

AC:

14858

AN:

44374

Middle Eastern (MID)

AF:

0.287

AC:

1499

AN:

5226

European-Non Finnish (NFE)

AF:

0.251

AC:

266933

AN:

1061444

Other (OTH)

AF:

0.279

AC:

15875

AN:

56800

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

14226

28451

42677

56902

71128

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9322

18644

27966

37288

46610

<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:

0.265

AC:

40224

AN:

152008

Hom.:

5641

Cov.:

AF XY:

0.273

AC XY:

20275

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.185

AC:

7665

AN:

41478

American (AMR)

AF:

0.329

AC:

5040

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

1195

AN:

3468

East Asian (EAS)

AF:

0.365

AC:

1880

AN:

5144

South Asian (SAS)

AF:

0.399

AC:

1918

AN:

4806

European-Finnish (FIN)

AF:

0.344

AC:

3638

AN:

10562

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.262

AC:

17835

AN:

67946

Other (OTH)

AF:

0.291

AC:

612

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1462

2923

4385

5846

7308

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.264

Hom.:

16456

Bravo

AF:

0.259

Asia WGS

AF:

0.365

AC:

1270

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

MHC class I deficiency

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

1.7

(source)

DANN

Benign

0.73

PhyloP100

-0.073

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over