6-29816415-C-G

Variant names:

• chr6-29816415-C-G
• rs1633097
• ENST00000849927.1:n.27-9963G>C

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.27-9963G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,682 control chromosomes in the GnomAD database, including 18,762 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 0.49 (18762 hom., cov: 33)
• Consequence: HLA-F-AS1 ENST00000849927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684
• Publications: 8 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 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.27-9963G>C		intron_variant	Intron 1 of 3
HLA-F-AS1	ENST00000849935.1	n.231-9963G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74694 AN: 151566 Hom.: 18733 Cov.: 33

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.493 AC: 74768 AN: 151682 Hom.: 18762 Cov.: 33 AF XY: 0.488 AC XY: 36194 AN XY: 74108

African (AFR) AF: 0.601 AC: 24896 AN: 41402

American (AMR) AF: 0.552 AC: 8423 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2081 AN: 3436

East Asian (EAS) AF: 0.437 AC: 2243 AN: 5136

South Asian (SAS) AF: 0.565 AC: 2685 AN: 4754

European-Finnish (FIN) AF: 0.316 AC: 3335 AN: 10548

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29490 AN: 67838

Other (OTH) AF: 0.521 AC: 1099 AN: 2108

Alfa AF: 0.245 Hom.: 398

Bravo AF: 0.515

Asia WGS AF: 0.566 AC: 1971 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	2.1
DANN	Benign	0.26
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs1633097; hg19: chr6-29784192;