ENST00000849873.1:n.421+14000C>T

Variant summary

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

The ENST00000849873.1(HLA-F-AS1):​n.421+14000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,082 control chromosomes in the GnomAD database, including 9,529 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 0.35 ( 9529 hom., cov: 32)

Consequence

HLA-F-AS1
ENST00000849873.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700

Publications

18 publications found
Variant links:
Genes affected
HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HLA-F-AS1ENST00000849873.1 linkn.421+14000C>T intron_variant Intron 1 of 1
HLA-F-AS1ENST00000849874.1 linkn.403+14000C>T intron_variant Intron 1 of 1
HLA-F-AS1ENST00000849875.1 linkn.354+14000C>T intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.345
AC:
52461
AN:
151964
Hom.:
9521
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.463
Gnomad AMI
AF:
0.204
Gnomad AMR
AF:
0.323
Gnomad ASJ
AF:
0.417
Gnomad EAS
AF:
0.194
Gnomad SAS
AF:
0.327
Gnomad FIN
AF:
0.197
Gnomad MID
AF:
0.415
Gnomad NFE
AF:
0.312
Gnomad OTH
AF:
0.354
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.345
AC:
52491
AN:
152082
Hom.:
9529
Cov.:
32
AF XY:
0.339
AC XY:
25189
AN XY:
74342
show subpopulations
African (AFR)
AF:
0.463
AC:
19176
AN:
41446
American (AMR)
AF:
0.323
AC:
4929
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.417
AC:
1449
AN:
3472
East Asian (EAS)
AF:
0.194
AC:
1006
AN:
5182
South Asian (SAS)
AF:
0.327
AC:
1579
AN:
4828
European-Finnish (FIN)
AF:
0.197
AC:
2088
AN:
10576
Middle Eastern (MID)
AF:
0.412
AC:
121
AN:
294
European-Non Finnish (NFE)
AF:
0.312
AC:
21221
AN:
67980
Other (OTH)
AF:
0.349
AC:
736
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1732
3464
5197
6929
8661
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
524
1048
1572
2096
2620
<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:
0.324
Hom.:
7176
Bravo
AF:
0.361
Asia WGS
AF:
0.257
AC:
896
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.4
DANN
Benign
0.47
PhyloP100
0.0070

Splicing

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

Publications

Other links and lift over

dbSNP: rs1614309; hg19: chr6-29745884; API