6-29772260-A-G

Variant names:

• chr6-29772260-A-G
• rs1633038
• ENST00000849873.1:n.421+19847T>C

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+19847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,178 control chromosomes in the GnomAD database, including 58,071 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 0.87 (58071 hom., cov: 31)
• Consequence: HLA-F-AS1 ENST00000849873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 13 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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	ENST00000849873.1	n.421+19847T>C		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849874.1	n.403+19847T>C		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849875.1	n.354+19847T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132364 AN: 152060 Hom.: 58000 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.871 AC: 132494 AN: 152178 Hom.: 58071 Cov.: 31 AF XY: 0.867 AC XY: 64463 AN XY: 74380

African (AFR) AF: 0.927 AC: 38513 AN: 41524

American (AMR) AF: 0.910 AC: 13925 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3141 AN: 3472

East Asian (EAS) AF: 0.986 AC: 5114 AN: 5186

South Asian (SAS) AF: 0.937 AC: 4516 AN: 4818

European-Finnish (FIN) AF: 0.693 AC: 7317 AN: 10566

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57060 AN: 67996

Other (OTH) AF: 0.886 AC: 1871 AN: 2112

Alfa AF: 0.860 Hom.: 103239

Bravo AF: 0.890

Asia WGS AF: 0.958 AC: 3333 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	1.9
DANN	Benign	0.29
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs1633038; hg19: chr6-29740037;