GeneBe

rs2523848

Variant names:

Variant summary

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

The ENST00000426185.2(HCG22):​n.1559+417G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,076 control chromosomes in the GnomAD database, including 3,734 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 0.21 ( 3734 hom., cov: 31)

Consequence

HCG22
ENST00000426185.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.208

Publications

11 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=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HCG22NR_003948.3 linkn.1701+417G>A intron_variant Intron 3 of 3
HCG22NR_145427.2 linkn.1193+417G>A intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HCG22ENST00000426185.2 linkn.1559+417G>A intron_variant Intron 2 of 2 2
HCG22ENST00000562344.2 linkn.1287+417G>A intron_variant Intron 2 of 2 5
HCG22ENST00000565192.1 linkn.1192+417G>A intron_variant Intron 3 of 3 2

Frequencies

GnomAD3 genomes
AF:
0.211
AC:
31990
AN:
151958
Hom.:
3726
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.276
Gnomad AMI
AF:
0.0890
Gnomad AMR
AF:
0.214
Gnomad ASJ
AF:
0.438
Gnomad EAS
AF:
0.281
Gnomad SAS
AF:
0.364
Gnomad FIN
AF:
0.135
Gnomad MID
AF:
0.263
Gnomad NFE
AF:
0.154
Gnomad OTH
AF:
0.246
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.211
AC:
32026
AN:
152076
Hom.:
3734
Cov.:
31
AF XY:
0.213
AC XY:
15869
AN XY:
74360
show subpopulations
African (AFR)
AF:
0.276
AC:
11437
AN:
41444
American (AMR)
AF:
0.214
AC:
3268
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
0.438
AC:
1517
AN:
3466
East Asian (EAS)
AF:
0.281
AC:
1455
AN:
5178
South Asian (SAS)
AF:
0.366
AC:
1761
AN:
4818
European-Finnish (FIN)
AF:
0.135
AC:
1434
AN:
10584
Middle Eastern (MID)
AF:
0.259
AC:
76
AN:
294
European-Non Finnish (NFE)
AF:
0.154
AC:
10478
AN:
67988
Other (OTH)
AF:
0.245
AC:
519
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
1282
2564
3845
5127
6409
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
346
692
1038
1384
1730
<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:
0.185
Hom.:
2882
Bravo
AF:
0.215
Asia WGS
AF:
0.339
AC:
1177
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.2
DANN
Benign
0.30
PhyloP100
-0.21

Splicing

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

Publications

Other links and lift over

dbSNP: rs2523848; hg19: chr6-31025104; API