rs34260811

Variant names:

• chr6-29747555-C-A
• rs34260811
• ENST00000399247.6:n.151-130G>T

Variant summary

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

The ENST00000399247.6(HLA-F-AS1):​n.151-130G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 151,346 control chromosomes in the GnomAD database, including 3,887 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 (3870 hom., cov: 28)
  • Exomes 𝑓: 0.25 (17 hom.)
• Consequence: HLA-F-AS1 ENST00000399247.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 9 publications found

Genes affected

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

MICE (HGNC:7094): (MHC class I polypeptide-related sequence E (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399247.6. 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
	HLA-F-AS1	NR_026972.1		n.151-130G>T		intron	N/A
	HLA-F-AS1	NR_026973.1		n.150+1345G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000399247.6	TSL:6	n.151-130G>T		intron	N/A
	HLA-F-AS1	ENST00000434086.2	TSL:6	n.353+5286G>T		intron	N/A
	HLA-F-AS1	ENST00000458236.1	TSL:6	n.94+1345G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33817 AN: 150782 Hom.: 3869 Cov.: 28

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.247 AC: 111 AN: 450 Hom.: 17 AF XY: 0.242 AC XY: 72 AN XY: 298

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 3 AN: 6

South Asian (SAS) AF: 0.107 AC: 3 AN: 28

European-Finnish (FIN) AF: 0.344 AC: 44 AN: 128

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.214 AC: 50 AN: 234

Other (OTH) AF: 0.262 AC: 11 AN: 42

GnomAD4 genome AF: 0.224 AC: 33827 AN: 150896 Hom.: 3870 Cov.: 28 AF XY: 0.225 AC XY: 16568 AN XY: 73674

African (AFR) AF: 0.180 AC: 7375 AN: 41002

American (AMR) AF: 0.201 AC: 3041 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3464

East Asian (EAS) AF: 0.365 AC: 1857 AN: 5090

South Asian (SAS) AF: 0.161 AC: 774 AN: 4796

European-Finnish (FIN) AF: 0.294 AC: 3043 AN: 10340

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16416 AN: 67762

Other (OTH) AF: 0.186 AC: 389 AN: 2092

Alfa AF: 0.233 Hom.: 3832

Bravo AF: 0.218

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.50
PhyloP100		-0.051
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Other links and lift over

dbSNP: rs34260811; hg19: chr6-29715332;