6-31200150-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000383331.4(HCG27):n.124-2222C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HCG27
ENST00000383331.4 intron
ENST00000383331.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.878
Publications
0 publications found
Genes affected
HCG27 (HGNC:27366): (HLA complex group 27)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| HCG27 | NR_026791.1 | n.124-2222C>A | intron_variant | Intron 1 of 1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| HCG27 | ENST00000383331.4 | n.124-2222C>A | intron_variant | Intron 1 of 1 | 1 | |||||
| HCG27 | ENST00000638546.2 | n.167-2222C>A | intron_variant | Intron 1 of 1 | 1 | |||||
| HCG27 | ENST00000414008.3 | n.257C>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 4 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 64Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 48
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
64
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
48
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
0
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
4
Middle Eastern (MID)
AF:
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
AC:
0
AN:
50
Other (OTH)
AF:
AC:
0
AN:
6
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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