6-32828876-C-A

Position:

• chr6-32828876-C-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001290043.2(TAP2):​c.*30G>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 0.268 in 1,524,222 control chromosomes in the GnomAD database, including 57,377 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.26 (5641 hom., cov: 31)
  • Exomes 𝑓: 0.27 (51736 hom.)
• Consequence: TAP2 NM_001290043.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0730

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BP6: Variant 6-32828876-C-A is Benign according to our data. Variant chr6-32828876-C-A is described in ClinVar as [Benign]. Clinvar id is 403509.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-32828876-C-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAP2	NM_001290043.2	c.*30G>T		3_prime_UTR_variant	12/12	ENST00000374897.4
TAP2	NM_018833.3	c.1932+524G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAP2	ENST00000374897.4	c.*30G>T		3_prime_UTR_variant	12/12	1	NM_001290043.2	A2

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40190 AN: 151888 Hom.: 5630 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.291

GnomAD3 exomes AF: 0.314 AC: 46386 AN: 147522 Hom.: 7687 AF XY: 0.316 AC XY: 25059 AN XY: 79270

Gnomad AFR exome AF: 0.177

Gnomad AMR exome AF: 0.355

Gnomad ASJ exome AF: 0.343

Gnomad EAS exome AF: 0.362

Gnomad SAS exome AF: 0.394

Gnomad FIN exome AF: 0.341

Gnomad NFE exome AF: 0.262

Gnomad OTH exome AF: 0.299

GnomAD4 exome AF: 0.269 AC: 368871 AN: 1372214 Hom.: 51736 Cov.: 38 AF XY: 0.272 AC XY: 182858 AN XY: 671772

Gnomad4 AFR exome AF: 0.184

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.349

Gnomad4 EAS exome AF: 0.354

Gnomad4 SAS exome AF: 0.393

Gnomad4 FIN exome AF: 0.335

Gnomad4 NFE exome AF: 0.251

Gnomad4 OTH exome AF: 0.279

GnomAD4 genome AF: 0.265 AC: 40224 AN: 152008 Hom.: 5641 Cov.: 31 AF XY: 0.273 AC XY: 20275 AN XY: 74286

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.291

Alfa AF: 0.264 Hom.: 5991

Bravo AF: 0.259

Asia WGS AF: 0.365 AC: 1270 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

MHC class I deficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	1.7
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs241449; hg19: chr6-32796653;