ENST00000399247.6:n.429-1559A>G

Variant names:

• chr6-29740445-T-C
• rs1610603
• ENST00000399247.6:n.429-1559A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000399247.6(HLA-F-AS1):​n.429-1559A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,232 control chromosomes in the GnomAD database, including 51,097 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 0.82 (51097 hom., cov: 34)
• Consequence: HLA-F-AS1 ENST00000399247.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 20 publications found

Genes affected

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-F-AS1	NR_026972.1	n.429-1559A>G		intron_variant	Intron 2 of 5
HLA-F-AS1	NR_026973.1	n.150+8455A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-F-AS1	ENST00000399247.6	n.429-1559A>G		intron_variant	Intron 2 of 5	6
HLA-F-AS1	ENST00000434086.2	n.354-1559A>G		intron_variant	Intron 1 of 3	6
HLA-F-AS1	ENST00000458236.1	n.350-1559A>G		intron_variant	Intron 2 of 5	6

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124226 AN: 152114 Hom.: 51036 Cov.: 34

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.817 AC: 124346 AN: 152232 Hom.: 51097 Cov.: 34 AF XY: 0.815 AC XY: 60633 AN XY: 74408

African (AFR) AF: 0.789 AC: 32772 AN: 41518

American (AMR) AF: 0.867 AC: 13265 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3035 AN: 3470

East Asian (EAS) AF: 0.983 AC: 5108 AN: 5194

South Asian (SAS) AF: 0.928 AC: 4480 AN: 4828

European-Finnish (FIN) AF: 0.691 AC: 7297 AN: 10564

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55626 AN: 68028

Other (OTH) AF: 0.824 AC: 1744 AN: 2116

Alfa AF: 0.825 Hom.: 132727

Bravo AF: 0.828

Asia WGS AF: 0.939 AC: 3266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.63
PhyloP100		-2.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1610603; hg19: chr6-29708222;