Genetic Variant HLA-F-AS1:n.26+9176G>A (chr6-29819295-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000849927.1(HLA-F-AS1):n.26+9176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,212 control chromosomes in the GnomAD database, including 59,328 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 0.88 ( 59328 hom., cov: 32)

Consequence

HLA-F-AS1
ENST00000849927.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.63

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=-1.05).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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-AS1	ENST00000849927.1 link	n.26+9176G>A		intron_variant	Intron 1 of 3
HLA-F-AS1	ENST00000849935.1 link	n.230+8425G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.880

AC:

133885

AN:

152094

Hom.:

59258

Cov.:

show subpopulations

Gnomad AFR

AF:

0.930

Gnomad AMI

AF:

0.852

Gnomad AMR

AF:

0.916

Gnomad ASJ

AF:

0.905

Gnomad EAS

AF:

0.986

Gnomad SAS

AF:

0.938

Gnomad FIN

AF:

0.726

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.852

Gnomad OTH

AF:

0.891

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

GnomAD4 genome

AF:

0.880

AC:

134014

AN:

152212

Hom.:

59328

Cov.:

AF XY:

0.877

AC XY:

65222

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.930

AC:

38639

AN:

41540

American (AMR)

AF:

0.917

AC:

14020

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.905

AC:

3137

AN:

3468

East Asian (EAS)

AF:

0.986

AC:

5113

AN:

5184

South Asian (SAS)

AF:

0.938

AC:

4532

AN:

4830

European-Finnish (FIN)

AF:

0.726

AC:

7672

AN:

10568

Middle Eastern (MID)

AF:

0.908

AC:

267

AN:

294

European-Non Finnish (NFE)

AF:

0.852

AC:

57972

AN:

68008

Other (OTH)

AF:

0.893

AC:

1885

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

792

1583

2375

3166

3958

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

898

1796

2694

3592

4490

<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:

0.876

Hom.:

53529

Bravo

AF:

0.898

Asia WGS

AF:

0.961

AC:

3343

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.52

(source)

DANN

Benign

0.44

PhyloP100

-1.6

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