rs17875395
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000443049.1(HCG4P8):n.920C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 355,054 control chromosomes in the GnomAD database, including 505 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 0.052 ( 288 hom., cov: 32)
Exomes 𝑓: 0.037 ( 217 hom. )
Consequence
HCG4P8
ENST00000443049.1 non_coding_transcript_exon
ENST00000443049.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.314
Genes affected
HCG4P8 (HGNC:22927): (HLA complex group 4 pseudogene 8)
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=-0.95).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0805 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HLA-G | NM_001363567.2 | c.7-391G>A | intron_variant | ||||
HLA-G | NM_001384280.1 | c.7-391G>A | intron_variant | ||||
HLA-G | NM_002127.6 | c.-112-288G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCG4P8 | ENST00000443049.1 | n.920C>T | non_coding_transcript_exon_variant | 1/1 | |||||
HLA-G | ENST00000376828.6 | c.7-391G>A | intron_variant | A2 | |||||
HLA-G | ENST00000428701.6 | n.67-288G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0517 AC: 7859AN: 152094Hom.: 282 Cov.: 32
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GnomAD4 exome AF: 0.0370 AC: 7508AN: 202842Hom.: 217 Cov.: 0 AF XY: 0.0364 AC XY: 4088AN XY: 112168
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GnomAD4 genome ? AF: 0.0518 AC: 7879AN: 152212Hom.: 288 Cov.: 32 AF XY: 0.0493 AC XY: 3673AN XY: 74428
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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