GeneBe

rs9262639

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000426185.2(HCG22):​n.1560-1176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,046 control chromosomes in the GnomAD database, including 3,862 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 0.22 ( 3862 hom., cov: 31)

Consequence

HCG22
ENST00000426185.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.486

Publications

15 publications found
Variant links:
Genes affected
HCG22 (HGNC:27780): (HLA complex group 22 (non-protein coding)) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HCG22NR_003948.3 linkn.1702-1176C>T intron_variant Intron 3 of 3
HCG22NR_145427.2 linkn.1194-1176C>T intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HCG22ENST00000426185.2 linkn.1560-1176C>T intron_variant Intron 2 of 2 2
HCG22ENST00000562344.2 linkn.1288-1176C>T intron_variant Intron 2 of 2 5
HCG22ENST00000565192.1 linkn.1193-1176C>T intron_variant Intron 3 of 3 2

Frequencies

GnomAD3 genomes
AF:
0.223
AC:
33892
AN:
151928
Hom.:
3864
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.186
Gnomad AMI
AF:
0.299
Gnomad AMR
AF:
0.253
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.191
Gnomad SAS
AF:
0.219
Gnomad FIN
AF:
0.293
Gnomad MID
AF:
0.291
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.238
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.223
AC:
33894
AN:
152046
Hom.:
3862
Cov.:
31
AF XY:
0.224
AC XY:
16652
AN XY:
74312
show subpopulations
African (AFR)
AF:
0.186
AC:
7719
AN:
41476
American (AMR)
AF:
0.252
AC:
3857
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.202
AC:
702
AN:
3470
East Asian (EAS)
AF:
0.191
AC:
988
AN:
5166
South Asian (SAS)
AF:
0.219
AC:
1054
AN:
4816
European-Finnish (FIN)
AF:
0.293
AC:
3084
AN:
10536
Middle Eastern (MID)
AF:
0.282
AC:
83
AN:
294
European-Non Finnish (NFE)
AF:
0.230
AC:
15636
AN:
67982
Other (OTH)
AF:
0.236
AC:
499
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1384
2768
4153
5537
6921
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
356
712
1068
1424
1780
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.230
Hom.:
7131
Bravo
AF:
0.219
Asia WGS
AF:
0.175
AC:
612
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
7.6
DANN
Benign
0.87
PhyloP100
-0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs9262639; hg19: chr6-31026009; API