Genetic Variant ENST00000849927.1:n.335+4838G>A (chr6-29716167-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.335+4838G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 152,066 control chromosomes in the GnomAD database, including 14,887 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 0.44 ( 14887 hom., cov: 32)

Consequence

HLA-F-AS1
ENST00000849927.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.583

Publications

37 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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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	ENST00000849927.1 link	n.335+4838G>A	intron_variant	Intron 3 of 3
HLA-F-AS1	ENST00000849929.1 link	n.149-7393G>A	intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849930.1 link	n.265+4858G>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

66936

AN:

151946

Hom.:

14875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.444

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.433

Gnomad ASJ

AF:

0.530

Gnomad EAS

AF:

0.342

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.436

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.456

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

GnomAD4 genome

AF:

0.440

AC:

66974

AN:

152066

Hom.:

14887

Cov.:

AF XY:

0.438

AC XY:

32532

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.444

AC:

18410

AN:

41462

American (AMR)

AF:

0.433

AC:

6612

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.530

AC:

1838

AN:

3470

East Asian (EAS)

AF:

0.342

AC:

1769

AN:

5176

South Asian (SAS)

AF:

0.302

AC:

1456

AN:

4826

European-Finnish (FIN)

AF:

0.436

AC:

4612

AN:

10568

Middle Eastern (MID)

AF:

0.456

AC:

134

AN:

294

European-Non Finnish (NFE)

AF:

0.453

AC:

30808

AN:

67972

Other (OTH)

AF:

0.453

AC:

955

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1921

3842

5763

7684

9605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

596

1192

1788

2384

2980

<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:

0.452

Hom.:

53570

Bravo

AF:

0.446

Asia WGS

AF:

0.321

AC:

1116

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

3.7

(source)

DANN

Benign

0.16

PhyloP100

-0.58

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