rs241455

chr6-32828242-C-Achr6-32828242-C-Gchr6-32828242-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001290043.2(TAP2):c.*664G>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 0.249 in 972,548 control chromosomes in the GnomAD database, including 31,368 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 0.26 (5605 hom., cov: 32)
  • Exomes 𝑓: 0.25 (25763 hom.)
• Consequence: TAP2 NM_001290043.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAP2	NM_001290043.2	c.*664G>T		3_prime_UTR_variant	12/12	ENST00000374897.4
TAP2	NM_018833.3	c.1932+1158G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAP2	ENST00000374897.4	c.*664G>T		3_prime_UTR_variant	12/12	1	NM_001290043.2	A2

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40086 AN: 151880 Hom.: 5595 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.246 AC: 202220 AN: 820550 Hom.: 25763 Cov.: 16 AF XY: 0.246 AC XY: 93484 AN XY: 379278

Gnomad4 AFR exome AF: 0.178

Gnomad4 AMR exome AF: 0.317

Gnomad4 ASJ exome AF: 0.346

Gnomad4 EAS exome AF: 0.350

Gnomad4 SAS exome AF: 0.408

Gnomad4 FIN exome AF: 0.332

Gnomad4 NFE exome AF: 0.243

Gnomad4 OTH exome AF: 0.260

GnomAD4 genome AF: 0.264 AC: 40120 AN: 151998 Hom.: 5605 Cov.: 32 AF XY: 0.272 AC XY: 20233 AN XY: 74294

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.290

Alfa AF: 0.234 Hom.: 1855

Bravo AF: 0.258

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.2
Dann	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs241455; hg19: chr6-32796019;