Genetic Variant HLA-F-AS1:n.1128T>C (chr6-29737882-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000434086.2(HLA-F-AS1):n.1128T>C 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 0.394 in 152,062 control chromosomes in the GnomAD database, including 12,015 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 0.39 ( 12007 hom., cov: 31)

Exomes 𝑓: 0.53 ( 8 hom. )

Consequence

HLA-F-AS1
ENST00000434086.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.288

Publications

65 publications found

Variant links:

Genes affected

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

HLA-F-AS1 links:

HLA-F (HGNC:4963): (major histocompatibility complex, class I, F) This gene belongs to the HLA class I heavy chain paralogues. It encodes a non-classical heavy chain that forms a heterodimer with a beta-2 microglobulin light chain, with the heavy chain anchored in the membrane. Unlike most other HLA heavy chains, this molecule is localized in the endoplasmic reticulum and Golgi apparatus, with a small amount present at the cell surface in some cell types. It contains a divergent peptide-binding groove, and is thought to bind a restricted subset of peptides for immune presentation. This gene exhibits few polymorphisms. Multiple transcript variants encoding different isoforms have been found for this gene. These variants lack a coding exon found in transcripts from other HLA paralogues due to an altered splice acceptor site, resulting in a shorter cytoplasmic domain. [provided by RefSeq, Jul 2008]

HLA-F 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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
HLA-F-AS1	NR_026972.1 link	n.1235+84T>C	intron_variant	Intron 4 of 5
HLA-F-AS1	NR_026973.1 link	n.151-10743T>C	intron_variant	Intron 1 of 1
HLA-F	XM_017010813.2 link	c.1159-240A>G	intron_variant	Intron 7 of 7	XP_016866302.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
HLA-F-AS1	ENST00000434086.2 link	n.1128T>C	non_coding_transcript_exon_variant	Exon 4 of 4	6
HLA-F-AS1	ENST00000849904.1 link	n.519T>C	non_coding_transcript_exon_variant	Exon 3 of 3
HLA-F-AS1	ENST00000849906.1 link	n.1137T>C	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.394

AC:

59885

AN:

151884

Hom.:

11988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.409

Gnomad AMR

AF:

0.415

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.291

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.397

GnomAD4 exome

AF:

0.534

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.521

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.394

AC:

59941

AN:

152004

Hom.:

12007

Cov.:

AF XY:

0.394

AC XY:

29266

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.308

AC:

12782

AN:

41464

American (AMR)

AF:

0.415

AC:

6341

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

1735

AN:

3468

East Asian (EAS)

AF:

0.424

AC:

2184

AN:

5152

South Asian (SAS)

AF:

0.293

AC:

1415

AN:

4822

European-Finnish (FIN)

AF:

0.428

AC:

4525

AN:

10570

Middle Eastern (MID)

AF:

0.340

AC:

100

AN:

294

European-Non Finnish (NFE)

AF:

0.436

AC:

29655

AN:

67942

Other (OTH)

AF:

0.395

AC:

833

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1870

3740

5609

7479

9349

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

556

1112

1668

2224

2780

<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:

0.421

Hom.:

46279

Bravo

AF:

0.393

Asia WGS

AF:

0.327

AC:

1136

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.7

(source)

DANN

Benign

0.70

PhyloP100

-0.29

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over