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GeneBe

rs3077

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001242525.2(HLA-DPA1):c.*115T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,222 control chromosomes in the GnomAD database, including 8,455 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 0.29 ( 8455 hom., cov: 32)
Exomes 𝑓: 0.12 ( 0 hom. )

Consequence

HLA-DPA1
NM_001242525.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.211
Variant links:
Genes affected
HLA-DPA1 (HGNC:4938): (major histocompatibility complex, class II, DP alpha 1) HLA-DPA1 belongs to the HLA class II alpha chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DPA) and a beta (DPB) chain, both anchored in the membrane. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa and its gene contains 5 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and the cytoplasmic tail. Within the DP molecule both the alpha chain and the beta chain contain the polymorphisms specifying the peptide binding specificities, resulting in up to 4 different molecules. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HLA-DPA1NM_033554.4 linkuse as main transcriptc.*115T>C 3_prime_UTR_variant 5/5 ENST00000692443.1
HLA-DPA1NM_001242525.2 linkuse as main transcriptc.*115T>C 3_prime_UTR_variant 6/6
HLA-DPA1NM_001242524.2 linkuse as main transcriptc.*115T>C 3_prime_UTR_variant 6/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HLA-DPA1ENST00000692443.1 linkuse as main transcriptc.*115T>C 3_prime_UTR_variant 5/5 NM_033554.4 P1
HLA-DPA1ENST00000419277.5 linkuse as main transcriptc.*115T>C 3_prime_UTR_variant 6/6 P1
HLA-DPA1ENST00000479107.1 linkuse as main transcriptn.4787T>C non_coding_transcript_exon_variant 2/2

Frequencies

GnomAD3 genomes
AF:
0.290
AC:
44035
AN:
151970
Hom.:
8436
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.498
Gnomad AMI
AF:
0.143
Gnomad AMR
AF:
0.246
Gnomad ASJ
AF:
0.169
Gnomad EAS
AF:
0.688
Gnomad SAS
AF:
0.344
Gnomad FIN
AF:
0.103
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.176
Gnomad OTH
AF:
0.302
GnomAD4 exome
AF:
0.119
AC:
16
AN:
134
Hom.:
0
Cov.:
0
AF XY:
0.125
AC XY:
12
AN XY:
96
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.500
Gnomad4 SAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.121
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.290
AC:
44085
AN:
152088
Hom.:
8455
Cov.:
32
AF XY:
0.287
AC XY:
21366
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.497
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.169
Gnomad4 EAS
AF:
0.689
Gnomad4 SAS
AF:
0.343
Gnomad4 FIN
AF:
0.103
Gnomad4 NFE
AF:
0.176
Gnomad4 OTH
AF:
0.309
Alfa
AF:
0.204
Hom.:
7222
Bravo
AF:
0.308
Asia WGS
AF:
0.452
AC:
1570
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
6.6
Dann
Benign
0.56

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.

Other links and lift over

dbSNP: rs3077; hg19: chr6-33033022; API