dbSNP rs1044043: TAP2:c.*2702T>G (chr6-32826204-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001290043.2(TAP2):c.*2702T>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 0.782 in 985,262 control chromosomes in the GnomAD database, including 302,058 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 0.82 ( 50702 hom., cov: 32)

Exomes 𝑓: 0.78 ( 251356 hom. )

Consequence

TAP2
NM_001290043.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.151

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 links:

ENSG00000250264 (HGNC:):

ENSG00000250264 links:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAP2	NM_001290043.2 link	c.*2702T>G		3_prime_UTR_variant	Exon 12 of 12	ENST00000374897.4	NP_001276972.1	Q03519-1Q5JNW1
TAP2	NM_018833.3 link	c.1932+3196T>G		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 link	c.*2702T>G		3_prime_UTR_variant	Exon 12 of 12	1	NM_001290043.2	ENSP00000364032.3		Q03519-1
ENSG00000250264	ENST00000452392.2 link	c.1932+3196T>G		intron_variant	Intron 11 of 14	2		ENSP00000391806.2		E7ENX8

Frequencies

GnomAD3 genomes

AF:

0.815

AC:

123939

AN:

152042

Hom.:

50659

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

0.873

Gnomad AMR

AF:

0.824

Gnomad ASJ

AF:

0.807

Gnomad EAS

AF:

0.861

Gnomad SAS

AF:

0.752

Gnomad FIN

AF:

0.806

Gnomad MID

AF:

0.801

Gnomad NFE

AF:

0.778

Gnomad OTH

AF:

0.834

GnomAD4 exome

AF:

0.776

AC:

646890

AN:

833102

Hom.:

251356

Cov.:

AF XY:

0.776

AC XY:

298587

AN XY:

384710

show subpopulations

Gnomad4 AFR exome

AF:

0.877

Gnomad4 AMR exome

AF:

0.840

Gnomad4 ASJ exome

AF:

0.816

Gnomad4 EAS exome

AF:

0.866

Gnomad4 SAS exome

AF:

0.760

Gnomad4 FIN exome

AF:

0.786

Gnomad4 NFE exome

AF:

0.774

Gnomad4 OTH exome

AF:

0.775

GnomAD4 genome

AF:

0.815

AC:

124043

AN:

152160

Hom.:

50702

Cov.:

AF XY:

0.815

AC XY:

60600

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.875

Gnomad4 AMR

AF:

0.824

Gnomad4 ASJ

AF:

0.807

Gnomad4 EAS

AF:

0.860

Gnomad4 SAS

AF:

0.751

Gnomad4 FIN

AF:

0.806

Gnomad4 NFE

AF:

0.778

Gnomad4 OTH

AF:

0.836

Alfa

AF:

0.791

Hom.:

52134

Bravo

AF:

0.821

Asia WGS

AF:

0.815

AC:

2837

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.2

DANN

Benign

0.49

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over