dbSNP rs1737010: HLA-F-AS1:n.421+2884T>G (chr6-29789223-A-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+2884T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,006 control chromosomes in the GnomAD database, including 13,500 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 0.41 ( 13500 hom., cov: 31)

Consequence

HLA-F-AS1
ENST00000849873.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.456

Publications

8 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 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+2884T>G	intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849874.1 link	n.403+2884T>G	intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849875.1 link	n.354+2884T>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

61534

AN:

151886

Hom.:

13478

Cov.:

show subpopulations

Gnomad AFR

AF:

0.569

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.415

Gnomad ASJ

AF:

0.495

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.429

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

GnomAD4 genome

AF:

0.405

AC:

61595

AN:

152006

Hom.:

13500

Cov.:

AF XY:

0.396

AC XY:

29444

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.569

AC:

23571

AN:

41438

American (AMR)

AF:

0.415

AC:

6339

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.495

AC:

1718

AN:

3470

East Asian (EAS)

AF:

0.200

AC:

1032

AN:

5152

South Asian (SAS)

AF:

0.356

AC:

1714

AN:

4816

European-Finnish (FIN)

AF:

0.207

AC:

2188

AN:

10572

Middle Eastern (MID)

AF:

0.520

AC:

153

AN:

294

European-Non Finnish (NFE)

AF:

0.350

AC:

23801

AN:

67964

Other (OTH)

AF:

0.423

AC:

892

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1766

3532

5297

7063

8829

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<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:

0.370

Hom.:

4176

Bravo

AF:

0.431

Asia WGS

AF:

0.288

AC:

1005

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.3

(source)

DANN

Benign

0.49

PhyloP100

-0.46

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