6-29721109-C-A

Variant names:

• chr6-29721109-C-A
• rs1632447
• ENST00000849927.1:n.231G>T

Variant summary

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

The ENST00000849927.1(HLA-F-AS1):​n.231G>T 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 0.826 in 151,852 control chromosomes in the GnomAD database, including 52,073 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 0.83 (52073 hom., cov: 30)
• Consequence: HLA-F-AS1 ENST00000849927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04
• Publications: 9 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=-1.06).
• 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-F-AS1	ENST00000849927.1	n.231G>T		non_coding_transcript_exon_variant	Exon 3 of 4
HLA-F-AS1	ENST00000849928.1	n.419G>T		non_coding_transcript_exon_variant	Exon 2 of 2
HLA-F-AS1	ENST00000849930.1	n.181G>T		non_coding_transcript_exon_variant	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125336 AN: 151734 Hom.: 52013 Cov.: 30

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.831

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

GnomAD4 genome AF: 0.826 AC: 125455 AN: 151852 Hom.: 52073 Cov.: 30 AF XY: 0.824 AC XY: 61117 AN XY: 74184

African (AFR) AF: 0.820 AC: 33883 AN: 41340

American (AMR) AF: 0.874 AC: 13352 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3038 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5092 AN: 5178

South Asian (SAS) AF: 0.928 AC: 4464 AN: 4808

European-Finnish (FIN) AF: 0.688 AC: 7215 AN: 10484

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55642 AN: 67986

Other (OTH) AF: 0.833 AC: 1753 AN: 2104

Alfa AF: 0.822 Hom.: 6657

Bravo AF: 0.838

Asia WGS AF: 0.941 AC: 3272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.5
DANN	Benign	0.26
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1632447; hg19: chr6-29688886;