6-29767916-A-G

Variant names:

• chr6-29767916-A-G
• rs1737046
• ENST00000850390.1:n.471A>G

Variant summary

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

The ENST00000850390.1(ENSG00000285761):​n.471A>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 0.658 in 151,520 control chromosomes in the GnomAD database, including 30,124 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 0.66 (30124 hom., cov: 33)
• Consequence: ENSG00000285761 ENST00000850390.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.76
• Publications: 14 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850390.1. 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
	ENSG00000285761	ENST00000850390.1		n.471A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000285761	ENST00000850391.1		n.514A>G		non_coding_transcript_exon	Exon 3 of 3
	HLA-F-AS1	ENST00000849873.1		n.421+24191T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99602 AN: 151404 Hom.: 30103 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.658 AC: 99666 AN: 151520 Hom.: 30124 Cov.: 33 AF XY: 0.650 AC XY: 48110 AN XY: 74026

African (AFR) AF: 0.706 AC: 29009 AN: 41108

American (AMR) AF: 0.633 AC: 9630 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2350 AN: 3462

East Asian (EAS) AF: 0.500 AC: 2575 AN: 5154

South Asian (SAS) AF: 0.522 AC: 2506 AN: 4798

European-Finnish (FIN) AF: 0.566 AC: 5981 AN: 10568

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.670 AC: 45529 AN: 67904

Other (OTH) AF: 0.644 AC: 1355 AN: 2104

Alfa AF: 0.713 Hom.: 45850

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.017
DANN	Benign	0.32
PhyloP100		-5.8

Splicing

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

Other links and lift over

dbSNP: rs1737046; hg19: chr6-29735693;