6-29745089-T-C

Variant names:

• chr6-29745089-T-C
• rs1633091
• ENST00000510438.1:n.471A>G

Variant summary

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

The ENST00000849910.1(HLA-F-AS1):​n.1037A>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 0.853 in 366,810 control chromosomes in the GnomAD database, including 134,401 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 0.81 (50540 hom., cov: 33)
  • Exomes 𝑓: 0.88 (83861 hom.)
• Consequence: HLA-F-AS1 ENST00000849910.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 8 publications found

Genes affected

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

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=-0.98).
• 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: ENST00000849910.1. 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
	HLA-F-AS1	NR_026972.1		n.428+2059A>G		intron	N/A
	HLA-F-AS1	NR_026973.1		n.150+3811A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICE	ENST00000510438.1	TSL:6	n.471A>G		non_coding_transcript_exon	Exon 3 of 6
	HLA-F-AS1	ENST00000849910.1		n.1037A>G		non_coding_transcript_exon	Exon 3 of 4
	HLA-F-AS1	ENST00000399247.6	TSL:6	n.428+2059A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123514 AN: 152052 Hom.: 50478 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.816

GnomAD4 exome AF: 0.882 AC: 189377 AN: 214640 Hom.: 83861 Cov.: 0 AF XY: 0.888 AC XY: 110731 AN XY: 124740

African (AFR) AF: 0.858 AC: 4079 AN: 4752

American (AMR) AF: 0.937 AC: 17813 AN: 19016

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3806 AN: 4096

East Asian (EAS) AF: 0.988 AC: 8089 AN: 8188

South Asian (SAS) AF: 0.951 AC: 33054 AN: 34768

European-Finnish (FIN) AF: 0.746 AC: 15802 AN: 21182

Middle Eastern (MID) AF: 0.858 AC: 1923 AN: 2242

European-Non Finnish (NFE) AF: 0.871 AC: 96353 AN: 110670

Other (OTH) AF: 0.870 AC: 8458 AN: 9726

GnomAD4 genome AF: 0.812 AC: 123634 AN: 152170 Hom.: 50540 Cov.: 33 AF XY: 0.811 AC XY: 60309 AN XY: 74396

African (AFR) AF: 0.780 AC: 32358 AN: 41478

American (AMR) AF: 0.861 AC: 13167 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3036 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5096 AN: 5182

South Asian (SAS) AF: 0.928 AC: 4480 AN: 4828

European-Finnish (FIN) AF: 0.690 AC: 7300 AN: 10576

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55454 AN: 68018

Other (OTH) AF: 0.818 AC: 1728 AN: 2112

Alfa AF: 0.819 Hom.: 33163

Bravo AF: 0.823

Asia WGS AF: 0.938 AC: 3263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.78
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1633091; hg19: chr6-29712866;