6-29817458-C-T

Variant names:

• chr6-29817458-C-T
• rs1619379
• ENST00000849927.1:n.27-11006G>A

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.27-11006G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,028 control chromosomes in the GnomAD database, including 12,125 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 (12125 hom., cov: 32)
• Consequence: HLA-F-AS1 ENST00000849927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 30 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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.27-11006G>A		intron_variant	Intron 1 of 3
HLA-F-AS1	ENST00000849935.1	n.230+10262G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60378 AN: 151910 Hom.: 12107 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.398 AC: 60441 AN: 152028 Hom.: 12125 Cov.: 32 AF XY: 0.393 AC XY: 29182 AN XY: 74308

African (AFR) AF: 0.391 AC: 16190 AN: 41446

American (AMR) AF: 0.426 AC: 6507 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1854 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1627 AN: 5184

South Asian (SAS) AF: 0.491 AC: 2361 AN: 4810

European-Finnish (FIN) AF: 0.263 AC: 2778 AN: 10570

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27758 AN: 67958

Other (OTH) AF: 0.418 AC: 883 AN: 2110

Alfa AF: 0.414 Hom.: 37196

Bravo AF: 0.408

Asia WGS AF: 0.382 AC: 1331 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	0.22
DANN	Benign	0.34
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1619379; hg19: chr6-29785235;