Variant rs241442 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001290043.2(TAP2):c.1932+9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,586,668 control chromosomes in the GnomAD database, including 58,881 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5465 hom., cov: 31)

Exomes 𝑓: 0.27 ( 53416 hom. )

Consequence

TAP2
NM_001290043.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.878

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 6-32829391-G-A is Benign according to our data. Variant chr6-32829391-G-A is described in ClinVar as [Benign]. Clinvar id is 403512.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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 link	c.1932+9C>T		intron_variant		ENST00000374897.4	NP_001276972.1	Q03519-1Q5JNW1
TAP2	NM_018833.3 link	c.1932+9C>T		intron_variant			NP_061313.2	Q03519-2Q9UP03

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAP2	ENST00000374897.4 link	c.1932+9C>T		intron_variant		1	NM_001290043.2	ENSP00000364032.3		Q03519-1
ENSG00000250264	ENST00000452392.2 link	c.1932+9C>T		intron_variant		2		ENSP00000391806.2		E7ENX8

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39662

AN:

151882

Hom.:

5455

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.359

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.287

GnomAD3 exomes

AF:

0.289

AC:

60170

AN:

208310

Hom.:

9054

AF XY:

0.294

AC XY:

32726

AN XY:

111450

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.283

Gnomad ASJ exome

AF:

0.345

Gnomad EAS exome

AF:

0.351

Gnomad SAS exome

AF:

0.389

Gnomad FIN exome

AF:

0.341

Gnomad NFE exome

AF:

0.252

Gnomad OTH exome

AF:

0.286

GnomAD4 exome

AF:

0.267

AC:

383734

AN:

1434668

Hom.:

53416

Cov.:

AF XY:

0.271

AC XY:

192733

AN XY:

710992

show subpopulations

Gnomad4 AFR exome

AF:

0.182

Gnomad4 AMR exome

AF:

0.284

Gnomad4 ASJ exome

AF:

0.349

Gnomad4 EAS exome

AF:

0.350

Gnomad4 SAS exome

AF:

0.391

Gnomad4 FIN exome

AF:

0.337

Gnomad4 NFE exome

AF:

0.251

Gnomad4 OTH exome

AF:

0.278

GnomAD4 genome

AF:

0.261

AC:

39693

AN:

152000

Hom.:

5465

Cov.:

AF XY:

0.269

AC XY:

19995

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.183

Gnomad4 AMR

AF:

0.306

Gnomad4 ASJ

AF:

0.344

Gnomad4 EAS

AF:

0.358

Gnomad4 SAS

AF:

0.398

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.262

Gnomad4 OTH

AF:

0.287

Alfa

AF:

0.254

Hom.:

3240

Bravo

AF:

0.253

Asia WGS

AF:

0.363

AC:

1262

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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

-0.81

CADD

Benign

0.14

DANN

Benign

0.59

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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