rs183585

Variant summary

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

The NM_001290043.2(TAP2):​c.1272+437C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,216 control chromosomes in the GnomAD database, including 4,697 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 ( 4697 hom., cov: 33)

Consequence

TAP2
NM_001290043.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.193
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=-0.74).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TAP2NM_001290043.2 linkuse as main transcriptc.1272+437C>T intron_variant ENST00000374897.4 NP_001276972.1
TAP2NM_018833.3 linkuse as main transcriptc.1272+437C>T intron_variant NP_061313.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TAP2ENST00000374897.4 linkuse as main transcriptc.1272+437C>T intron_variant 1 NM_001290043.2 ENSP00000364032 A2Q03519-1

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
37218
AN:
152098
Hom.:
4684
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.231
Gnomad AMI
AF:
0.192
Gnomad AMR
AF:
0.306
Gnomad ASJ
AF:
0.282
Gnomad EAS
AF:
0.254
Gnomad SAS
AF:
0.277
Gnomad FIN
AF:
0.185
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.244
Gnomad OTH
AF:
0.251
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37268
AN:
152216
Hom.:
4697
Cov.:
33
AF XY:
0.243
AC XY:
18051
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.231
Gnomad4 AMR
AF:
0.307
Gnomad4 ASJ
AF:
0.282
Gnomad4 EAS
AF:
0.253
Gnomad4 SAS
AF:
0.277
Gnomad4 FIN
AF:
0.185
Gnomad4 NFE
AF:
0.244
Gnomad4 OTH
AF:
0.251
Alfa
AF:
0.244
Hom.:
2073
Bravo
AF:
0.255
Asia WGS
AF:
0.292
AC:
1013
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
4.7
DANN
Benign
0.82

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: rs183585; hg19: chr6-32799673; API