6-33065245-A-G
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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
NM_001242525.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.211
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-DPA1 | NM_033554.4 | c.*115T>C | 3_prime_UTR_variant | 5/5 | ENST00000692443.1 | ||
HLA-DPA1 | NM_001242525.2 | c.*115T>C | 3_prime_UTR_variant | 6/6 | |||
HLA-DPA1 | NM_001242524.2 | c.*115T>C | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-DPA1 | ENST00000692443.1 | c.*115T>C | 3_prime_UTR_variant | 5/5 | NM_033554.4 | P1 | |||
HLA-DPA1 | ENST00000419277.5 | c.*115T>C | 3_prime_UTR_variant | 6/6 | P1 | ||||
HLA-DPA1 | ENST00000479107.1 | n.4787T>C | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? AF: 0.290 AC: 44035AN: 151970Hom.: 8436 Cov.: 32
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GnomAD4 exome AF: 0.119 AC: 16AN: 134Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 12AN XY: 96
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GnomAD4 genome ? AF: 0.290 AC: 44085AN: 152088Hom.: 8455 Cov.: 32 AF XY: 0.287 AC XY: 21366AN XY: 74358
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at