6-29741457-C-T

Variant names:

• chr6-29741457-C-T
• rs2743951
• ENST00000849877.1:n.1064G>A

Variant summary

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

The ENST00000849877.1(HLA-F-AS1):​n.1064G>A 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 0.403 in 151,704 control chromosomes in the GnomAD database, including 12,485 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 0.40 (12485 hom., cov: 32)
• Consequence: HLA-F-AS1 ENST00000849877.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 32 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-F-AS1	NR_026972.1	n.429-2571G>A		intron_variant	Intron 2 of 5
HLA-F-AS1	NR_026973.1	n.150+7443G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-F-AS1	ENST00000849877.1	n.1064G>A		non_coding_transcript_exon_variant	Exon 3 of 3
HLA-F-AS1	ENST00000849907.1	n.778G>A		non_coding_transcript_exon_variant	Exon 2 of 2
HLA-F-AS1	ENST00000849909.1	n.878G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61074 AN: 151590 Hom.: 12471 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.403 AC: 61125 AN: 151704 Hom.: 12485 Cov.: 32 AF XY: 0.404 AC XY: 29921 AN XY: 74140

African (AFR) AF: 0.310 AC: 12822 AN: 41376

American (AMR) AF: 0.469 AC: 7128 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2203 AN: 5180

South Asian (SAS) AF: 0.307 AC: 1474 AN: 4804

European-Finnish (FIN) AF: 0.439 AC: 4612 AN: 10512

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29828 AN: 67842

Other (OTH) AF: 0.403 AC: 851 AN: 2112

Alfa AF: 0.429 Hom.: 50861

Bravo AF: 0.401

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.40
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2743951; hg19: chr6-29709234;