chr6-28986516-G-A

Variant summary

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

The ENST00000759771.1(HCG15):​n.298G>A 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 0.0514 in 154,206 control chromosomes in the GnomAD database, including 337 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 ( 336 hom., cov: 32)
Exomes 𝑓: 0.0041 ( 1 hom. )

Consequence

HCG15
ENST00000759771.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Publications

32 publications found
Variant links:
Genes affected
HCG15 (HGNC:18361): (HLA complex group 15)

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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0882 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HCG15NR_135289.2 linkn.237-161G>A intron_variant Intron 1 of 2
HCG15NR_145490.1 linkn.422+10G>A intron_variant Intron 3 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HCG15ENST00000759771.1 linkn.298G>A non_coding_transcript_exon_variant Exon 3 of 5
HCG15ENST00000759779.1 linkn.423G>A non_coding_transcript_exon_variant Exon 3 of 5
HCG15ENST00000438190.1 linkn.224+10G>A intron_variant Intron 2 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.0521
AC:
7929
AN:
152152
Hom.:
336
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0174
Gnomad AMI
AF:
0.139
Gnomad AMR
AF:
0.0246
Gnomad ASJ
AF:
0.0207
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.0403
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0901
Gnomad OTH
AF:
0.0344
GnomAD4 exome
AF:
0.00413
AC:
8
AN:
1936
Hom.:
1
Cov.:
0
AF XY:
0.00302
AC XY:
3
AN XY:
994
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
0.00
AC:
0
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00270
AC:
5
AN:
1854
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.0517
AC:
3
AN:
58
Other (OTH)
AF:
0.00
AC:
0
AN:
20
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.408
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0520
AC:
7925
AN:
152270
Hom.:
336
Cov.:
32
AF XY:
0.0464
AC XY:
3452
AN XY:
74450
show subpopulations
African (AFR)
AF:
0.0174
AC:
722
AN:
41554
American (AMR)
AF:
0.0245
AC:
375
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
0.0207
AC:
72
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5178
South Asian (SAS)
AF:
0.000207
AC:
1
AN:
4824
European-Finnish (FIN)
AF:
0.0403
AC:
428
AN:
10608
Middle Eastern (MID)
AF:
0.00340
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
0.0901
AC:
6127
AN:
68012
Other (OTH)
AF:
0.0341
AC:
72
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
400
800
1200
1600
2000
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
94
188
282
376
470
<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:
0.0769
Hom.:
1244
Bravo
AF:
0.0500
Asia WGS
AF:
0.00404
AC:
15
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.9
DANN
Benign
0.77
PhyloP100
-0.076
Mutation Taster
=100/0
polymorphism

Splicing

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

Publications

Other links and lift over

dbSNP: rs3129791; hg19: chr6-28954293; API