6-29762865-A-G

Variant names:

• chr6-29762865-A-G
• rs1633048
• ENST00000648999.2:n.1447A>G

Variant summary

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

The ENST00000648999.2(ENSG00000285761):​n.1447A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,208 control chromosomes in the GnomAD database, including 50,952 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 (50952 hom., cov: 33)
• Consequence: ENSG00000285761 ENST00000648999.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 10 publications found

Genes affected

ENSG00000285761 (HGNC:):

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648999.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285761	ENST00000648999.2		n.1447A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000285761	ENST00000850392.1		n.750A>G		non_coding_transcript_exon	Exon 3 of 3
	HLA-F-AS1	ENST00000849873.1		n.421+29242T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124042 AN: 152090 Hom.: 50891 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.928

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: 0.816 AC: 124162 AN: 152208 Hom.: 50952 Cov.: 33 AF XY: 0.814 AC XY: 60559 AN XY: 74410

African (AFR) AF: 0.786 AC: 32616 AN: 41516

American (AMR) AF: 0.866 AC: 13243 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3037 AN: 3470

East Asian (EAS) AF: 0.983 AC: 5086 AN: 5172

South Asian (SAS) AF: 0.929 AC: 4486 AN: 4830

European-Finnish (FIN) AF: 0.691 AC: 7316 AN: 10588

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

European-Non Finnish (NFE) AF: 0.818 AC: 55618 AN: 68014

Other (OTH) AF: 0.825 AC: 1743 AN: 2114

Alfa AF: 0.823 Hom.: 119026

Bravo AF: 0.827

Asia WGS AF: 0.939 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.52
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1633048; hg19: chr6-29730642;