dbSNP rs1233335: HLA-F-AS1:n.26+2667G>C (chr6-29825804-C-G) – 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+2667G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0469 in 152,294 control chromosomes in the GnomAD database, including 202 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 0.047 ( 202 hom., cov: 32)

Consequence

HLA-F-AS1
ENST00000849927.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.383

Publications

4 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 (AFR) allele frequency at 95% confidence interval = 0.081 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+2667G>C		intron_variant	Intron 1 of 3
HLA-F-AS1	ENST00000849935.1 link	n.230+1916G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0468

AC:

7119

AN:

152176

Hom.:

199

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0831

Gnomad AMI

AF:

0.0319

Gnomad AMR

AF:

0.0548

Gnomad ASJ

AF:

0.0452

Gnomad EAS

AF:

0.00944

Gnomad SAS

AF:

0.0120

Gnomad FIN

AF:

0.00669

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0344

Gnomad OTH

AF:

0.0565

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

GnomAD4 genome

AF:

0.0469

AC:

7139

AN:

152294

Hom.:

202

Cov.:

AF XY:

0.0460

AC XY:

3423

AN XY:

74482

show subpopulations

African (AFR)

AF:

0.0833

AC:

3464

AN:

41574

American (AMR)

AF:

0.0548

AC:

838

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0452

AC:

157

AN:

3472

East Asian (EAS)

AF:

0.00946

AC:

AN:

5178

South Asian (SAS)

AF:

0.0120

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00669

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0344

AC:

2341

AN:

68020

Other (OTH)

AF:

0.0559

AC:

118

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

351

703

1054

1406

1757

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

210

280

350

<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:

0.0124

Hom.:

Bravo

AF:

0.0536

Asia WGS

AF:

0.0160

AC:

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

1.4

(source)

DANN

Benign

0.39

PhyloP100

-0.38

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