6-29779092-T-C

Variant names:

• chr6-29779092-T-C
• rs1633021
• ENST00000849873.1:n.421+13015A>G

Variant summary

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

The ENST00000849873.1(HLA-F-AS1):​n.421+13015A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,058 control chromosomes in the GnomAD database, including 3,630 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 0.22 (3630 hom., cov: 32)
• Consequence: HLA-F-AS1 ENST00000849873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514
• Publications: 38 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849873.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000849873.1		n.421+13015A>G		intron	N/A
	HLA-F-AS1	ENST00000849874.1		n.403+13015A>G		intron	N/A
	HLA-F-AS1	ENST00000849875.1		n.354+13015A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32931 AN: 151940 Hom.: 3631 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0678

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.217 AC: 32928 AN: 152058 Hom.: 3630 Cov.: 32 AF XY: 0.211 AC XY: 15699 AN XY: 74322

African (AFR) AF: 0.215 AC: 8923 AN: 41462

American (AMR) AF: 0.217 AC: 3309 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.0679 AC: 352 AN: 5182

South Asian (SAS) AF: 0.204 AC: 983 AN: 4816

European-Finnish (FIN) AF: 0.164 AC: 1733 AN: 10572

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16199 AN: 67958

Other (OTH) AF: 0.215 AC: 455 AN: 2112

Alfa AF: 0.236 Hom.: 17167

Bravo AF: 0.222

Asia WGS AF: 0.132 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1633021; hg19: chr6-29746869;