rs1632942
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001384290.1(HLA-G):c.619+45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 1,605,552 control chromosomes in the GnomAD database, including 225,030 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 0.55 ( 22833 hom., cov: 30)
Exomes 𝑓: 0.52 ( 202197 hom. )
Consequence
HLA-G
NM_001384290.1 intron
NM_001384290.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.18
Genes affected
HLA-G (HGNC:4964): (major histocompatibility complex, class I, G) HLA-G belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. HLA-G is expressed on fetal derived placental cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domain, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exon 6 encodes the cytoplasmic tail. [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=-0.89).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-G | NM_001384290.1 | c.619+45T>C | intron_variant | ENST00000360323.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HLA-G | ENST00000360323.11 | c.619+45T>C | intron_variant | NM_001384290.1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.547 AC: 82404AN: 150738Hom.: 22799 Cov.: 30
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GnomAD3 exomes AF: 0.544 AC: 134474AN: 247242Hom.: 38073 AF XY: 0.550 AC XY: 73823AN XY: 134148
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GnomAD4 exome AF: 0.522 AC: 759111AN: 1454694Hom.: 202197 Cov.: 37 AF XY: 0.528 AC XY: 382554AN XY: 723926
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GnomAD4 genome ? AF: 0.547 AC: 82488AN: 150858Hom.: 22833 Cov.: 30 AF XY: 0.544 AC XY: 40106AN XY: 73704
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at