chr6-32828974-T-C

Position:

chr6-32828974-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001290043.2(TAP2):c.1993A>G(p.Thr665Ala) variant causes a missense change. The variant allele was found at a frequency of 0.269 in 1,549,446 control chromosomes in the GnomAD database, including 58,603 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5642 hom., cov: 30)

Exomes 𝑓: 0.27 ( 52961 hom. )

Consequence

TAP2
NM_001290043.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 4.70

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.031624883).

BP6

Variant 6-32828974-T-C is Benign according to our data. Variant chr6-32828974-T-C is described in ClinVar as [Benign]. Clinvar id is 403511.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-32828974-T-C 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	Protein	UniProt
TAP2	NM_001290043.2 linkuse as main transcript	c.1993A>G	p.Thr665Ala	missense_variant	12/12	ENST00000374897.4	NP_001276972.1
TAP2	NM_018833.3 linkuse as main transcript	c.1932+426A>G		intron_variant			NP_061313.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAP2	ENST00000374897.4 linkuse as main transcript	c.1993A>G	p.Thr665Ala	missense_variant	12/12	1	NM_001290043.2	ENSP00000364032	A2	Q03519-1

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40167

AN:

151784

Hom.:

5632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.366

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.291

GnomAD3 exomes

AF:

0.313

AC:

47971

AN:

153132

Hom.:

7901

AF XY:

0.315

AC XY:

25954

AN XY:

82418

show subpopulations

Gnomad AFR exome

AF:

0.176

Gnomad AMR exome

AF:

0.355

Gnomad ASJ exome

AF:

0.345

Gnomad EAS exome

AF:

0.359

Gnomad SAS exome

AF:

0.394

Gnomad FIN exome

AF:

0.342

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.298

GnomAD4 exome

AF:

0.269

AC:

376632

AN:

1397544

Hom.:

52961

Cov.:

AF XY:

0.273

AC XY:

188203

AN XY:

689444

show subpopulations

Gnomad4 AFR exome

AF:

0.184

Gnomad4 AMR exome

AF:

0.347

Gnomad4 ASJ exome

AF:

0.350

Gnomad4 EAS exome

AF:

0.353

Gnomad4 SAS exome

AF:

0.393

Gnomad4 FIN exome

AF:

0.335

Gnomad4 NFE exome

AF:

0.252

Gnomad4 OTH exome

AF:

0.280

GnomAD4 genome

AF:

0.265

AC:

40199

AN:

151902

Hom.:

5642

Cov.:

AF XY:

0.273

AC XY:

20265

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.329

Gnomad4 ASJ

AF:

0.344

Gnomad4 EAS

AF:

0.366

Gnomad4 SAS

AF:

0.399

Gnomad4 FIN

AF:

0.345

Gnomad4 NFE

AF:

0.262

Gnomad4 OTH

AF:

0.292

Alfa

AF:

0.271

Hom.:

12023

Bravo

AF:

0.259

TwinsUK

AF:

0.230

AC:

851

ALSPAC

AF:

0.239

AC:

921

ESP6500AA

AF:

0.156

AC:

397

ESP6500EA

AF:

0.214

AC:

1026

ExAC

AF:

0.190

AC:

17273

Asia WGS

AF:

0.365

AC:

1269

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

MHC class I deficiency

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.26

CADD

Benign

DANN

Benign

0.89

DEOGEN2

Benign

0.38

.;T

Eigen

Benign

-0.51

Eigen_PC

Benign

-0.45

FATHMM_MKL

Uncertain

0.95

MetaRNN

Benign

0.032

T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.9

.;L

PrimateAI

Benign

0.47

PROVEAN

Uncertain

-3.4

.;D

REVEL

Benign

0.29

Sift

Benign

0.037

.;D

Sift4G

Uncertain

0.010

D;D

Polyphen

0.19

.;B

Vest4

0.082

ClinPred

0.042

GERP RS

3.4

Varity_R

0.067

gMVP

0.48

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over