Genetic Variant HLA-F-AS1:n.421+14291A>G (chr6-29777816-T-C) – ACMG Classification: Benign (-12 pts)

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+14291A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 152,234 control chromosomes in the GnomAD database, including 808 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 0.089 ( 808 hom., cov: 32)

Consequence

HLA-F-AS1
ENST00000849873.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.693

Publications

13 publications found

Variant links:

Genes affected

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

HLA-F-AS1 links:

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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
HLA-F-AS1	ENST00000849873.1 link	n.421+14291A>G	intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849874.1 link	n.403+14291A>G	intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849875.1 link	n.354+14291A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0886

AC:

13480

AN:

152116

Hom.:

796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0661

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.0951

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.0724

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.0706

Gnomad OTH

AF:

0.0917

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0888

AC:

13512

AN:

152234

Hom.:

808

Cov.:

AF XY:

0.0931

AC XY:

6933

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0663

AC:

2753

AN:

41544

American (AMR)

AF:

0.142

AC:

2175

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0951

AC:

330

AN:

3470

East Asian (EAS)

AF:

0.229

AC:

1184

AN:

5176

South Asian (SAS)

AF:

0.231

AC:

1117

AN:

4830

European-Finnish (FIN)

AF:

0.0724

AC:

767

AN:

10600

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0706

AC:

4799

AN:

67996

Other (OTH)

AF:

0.0997

AC:

211

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

621

1242

1863

2484

3105

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.0812

Hom.:

1998

Bravo

AF:

0.0888

Asia WGS

AF:

0.286

AC:

993

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.7

(source)

DANN

Benign

0.85

PhyloP100

0.69

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over