rs2857101

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001290043.2(TAP2):​c.*2007A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 985,176 control chromosomes in the GnomAD database, including 31,362 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 0.25 ( 5205 hom., cov: 32)
Exomes 𝑓: 0.25 ( 26157 hom. )

Consequence

TAP2
NM_001290043.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.166
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]

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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 (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TAP2NM_001290043.2 linkuse as main transcriptc.*2007A>G 3_prime_UTR_variant 12/12 ENST00000374897.4
TAP2NM_018833.3 linkuse as main transcriptc.1932+2501A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TAP2ENST00000374897.4 linkuse as main transcriptc.*2007A>G 3_prime_UTR_variant 12/121 NM_001290043.2 A2Q03519-1

Frequencies

GnomAD3 genomes
AF:
0.249
AC:
37807
AN:
152036
Hom.:
5199
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.140
Gnomad AMI
AF:
0.388
Gnomad AMR
AF:
0.315
Gnomad ASJ
AF:
0.339
Gnomad EAS
AF:
0.358
Gnomad SAS
AF:
0.387
Gnomad FIN
AF:
0.344
Gnomad MID
AF:
0.293
Gnomad NFE
AF:
0.260
Gnomad OTH
AF:
0.268
GnomAD4 exome
AF:
0.247
AC:
205931
AN:
833022
Hom.:
26157
Cov.:
33
AF XY:
0.247
AC XY:
95062
AN XY:
384678
show subpopulations
Gnomad4 AFR exome
AF:
0.141
Gnomad4 AMR exome
AF:
0.313
Gnomad4 ASJ exome
AF:
0.342
Gnomad4 EAS exome
AF:
0.349
Gnomad4 SAS exome
AF:
0.410
Gnomad4 FIN exome
AF:
0.338
Gnomad4 NFE exome
AF:
0.244
Gnomad4 OTH exome
AF:
0.256
GnomAD4 genome
AF:
0.249
AC:
37829
AN:
152154
Hom.:
5205
Cov.:
32
AF XY:
0.257
AC XY:
19140
AN XY:
74384
show subpopulations
Gnomad4 AFR
AF:
0.140
Gnomad4 AMR
AF:
0.315
Gnomad4 ASJ
AF:
0.339
Gnomad4 EAS
AF:
0.357
Gnomad4 SAS
AF:
0.387
Gnomad4 FIN
AF:
0.344
Gnomad4 NFE
AF:
0.260
Gnomad4 OTH
AF:
0.269
Alfa
AF:
0.268
Hom.:
8399
Bravo
AF:
0.241
Asia WGS
AF:
0.342
AC:
1190
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
5.7
DANN
Benign
0.79

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.

Other links and lift over

dbSNP: rs2857101; hg19: chr6-32794676; API