rs1044043

Variant names:

• chr6-32826204-A-C
• rs1044043
• NM_001290043.2:c.*2702T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32826204-A-C
• chr6-32826204-A-G
• chr6-32826204-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 23 publications found

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

ENSG00000250264 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001290043.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAP2	NM_001290043.2	MANE Select	c.*2702T>G		3_prime_UTR	Exon 12 of 12	NP_001276972.1
	TAP2	NM_018833.3		c.1932+3196T>G		intron	N/A	NP_061313.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAP2	ENST00000374897.4	TSL:1 MANE Select	c.*2702T>G		3_prime_UTR	Exon 12 of 12	ENSP00000364032.3
	ENSG00000250264	ENST00000452392.2	TSL:2	c.1932+3196T>G		intron	N/A	ENSP00000391806.2
	TAP2	ENST00000698440.1		c.*2702T>G		3_prime_UTR	Exon 13 of 13	ENSP00000513722.1

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123939 AN: 152042 Hom.: 50659 Cov.: 32

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.: 45 AF XY: 0.776 AC XY: 298587 AN XY: 384710

African (AFR) AF: 0.877 AC: 13848 AN: 15786

American (AMR) AF: 0.840 AC: 827 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 4206 AN: 5152

East Asian (EAS) AF: 0.866 AC: 3143 AN: 3630

South Asian (SAS) AF: 0.760 AC: 12504 AN: 16460

European-Finnish (FIN) AF: 0.786 AC: 217 AN: 276

Middle Eastern (MID) AF: 0.826 AC: 1338 AN: 1620

European-Non Finnish (NFE) AF: 0.774 AC: 589642 AN: 761898

Other (OTH) AF: 0.775 AC: 21165 AN: 27296

GnomAD4 genome AF: 0.815 AC: 124043 AN: 152160 Hom.: 50702 Cov.: 32 AF XY: 0.815 AC XY: 60600 AN XY: 74388

African (AFR) AF: 0.875 AC: 36322 AN: 41524

American (AMR) AF: 0.824 AC: 12599 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2802 AN: 3472

East Asian (EAS) AF: 0.860 AC: 4450 AN: 5174

South Asian (SAS) AF: 0.751 AC: 3625 AN: 4824

European-Finnish (FIN) AF: 0.806 AC: 8521 AN: 10576

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52928 AN: 67988

Other (OTH) AF: 0.836 AC: 1764 AN: 2110

Alfa AF: 0.789 Hom.: 150070

Bravo AF: 0.821

Asia WGS AF: 0.815 AC: 2837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.2
DANN	Benign	0.49
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1044043; hg19: chr6-32793981;