rs1057373

chr6-32845502-C-A

Variant summary

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

The NM_000593.6(TAP1):c.*77G>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 0.0902 in 1,497,186 control chromosomes in the GnomAD database, including 6,750 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 0.082 (584 hom., cov: 32)
  • Exomes 𝑓: 0.091 (6166 hom.)
• Consequence: TAP1 NM_000593.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

TAP1 (HGNC:43): (transporter 1, 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. The protein encoded by this gene is involved in the pumping of degraded cytosolic peptides across the endoplasmic reticulum into the membrane-bound compartment where class I molecules assemble. Mutations in this gene may be associated with ankylosing spondylitis, insulin-dependent diabetes mellitus, and celiac disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

PSMB8-AS1 (HGNC:39758): (PSMB8 antisense RNA 1 (head to head))

PSMB9 (HGNC:9546): (proteasome 20S subunit beta 9) The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. This gene is located in the class II region of the MHC (major histocompatibility complex). Expression of this gene is induced by gamma interferon and this gene product replaces catalytic subunit 1 (proteasome beta 6 subunit) in the immunoproteasome. Proteolytic processing is required to generate a mature subunit. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAP1	NM_000593.6	c.*77G>T		3_prime_UTR_variant	11/11	ENST00000354258.5
PSMB8-AS1	NR_037173.1	n.500C>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAP1	ENST00000354258.5	c.*77G>T		3_prime_UTR_variant	11/11	1	NM_000593.6	P1
PSMB8-AS1	ENST00000453426.2	n.274C>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12494 AN: 152096 Hom.: 577 Cov.: 32

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0764

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.0742

GnomAD4 exome AF: 0.0911 AC: 122579 AN: 1344972 Hom.: 6166 Cov.: 23 AF XY: 0.0932 AC XY: 62813 AN XY: 673660

Gnomad4 AFR exome AF: 0.0444

Gnomad4 AMR exome AF: 0.119

Gnomad4 ASJ exome AF: 0.0218

Gnomad4 EAS exome AF: 0.133

Gnomad4 SAS exome AF: 0.152

Gnomad4 FIN exome AF: 0.142

Gnomad4 NFE exome AF: 0.0841

Gnomad4 OTH exome AF: 0.0841

GnomAD4 genome AF: 0.0822 AC: 12519 AN: 152214 Hom.: 584 Cov.: 32 AF XY: 0.0854 AC XY: 6357 AN XY: 74416

Gnomad4 AFR AF: 0.0432

Gnomad4 AMR AF: 0.0774

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.0907

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0886 Hom.: 1272

Bravo AF: 0.0761

Asia WGS AF: 0.132 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	9.9
Dann	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1057373; hg19: chr6-32813279; COSMIC: COSV62754256; COSMIC: COSV62754256;