dbSNP rs1633030: HLA-F-AS1:n.421+14090A>G (chr6-29778017-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+14090A>G 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 152,010 control chromosomes in the GnomAD database, including 9,527 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 ( 9527 hom., cov: 32)

Consequence

HLA-F-AS1
ENST00000849873.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Publications

29 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=-1.01).

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	Effect	Exon rank
HLA-F-AS1	ENST00000849873.1 link	n.421+14090A>G	intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849874.1 link	n.403+14090A>G	intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849875.1 link	n.354+14090A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52444

AN:

151892

Hom.:

9519

Cov.:

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:

0.193

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:

52474

AN:

152010

Hom.:

9527

Cov.:

AF XY:

0.339

AC XY:

25180

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.463

AC:

19167

AN:

41442

American (AMR)

AF:

0.323

AC:

4933

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.417

AC:

1445

AN:

3466

East Asian (EAS)

AF:

0.193

AC:

998

AN:

5172

South Asian (SAS)

AF:

0.327

AC:

1576

AN:

4818

European-Finnish (FIN)

AF:

0.197

AC:

2082

AN:

10556

Middle Eastern (MID)

AF:

0.412

AC:

121

AN:

294

European-Non Finnish (NFE)

AF:

0.312

AC:

21230

AN:

67956

Other (OTH)

AF:

0.348

AC:

736

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1705

3410

5115

6820

8525

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

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:

0.332

Hom.:

29200

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

-1.0

CADD

Benign

0.40

(source)

DANN

Benign

0.69

PhyloP100

-1.0

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