chr6-29778017-T-C

Variant names:

• chr6-29778017-T-C
• rs1633030
• ENST00000849873.1:n.421+14090A>G

Variant summary

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

The ENST00000849873.1(HLA-F-AS1):​n.421+14090A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,010 control chromosomes in the GnomAD database, including 9,527 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 0.35 (9527 hom., cov: 32)
• Consequence: HLA-F-AS1 ENST00000849873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 29 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 (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849873.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000849873.1		n.421+14090A>G		intron	N/A
	HLA-F-AS1	ENST00000849874.1		n.403+14090A>G		intron	N/A
	HLA-F-AS1	ENST00000849875.1		n.354+14090A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52444 AN: 151892 Hom.: 9519 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.345 AC: 52474 AN: 152010 Hom.: 9527 Cov.: 32 AF XY: 0.339 AC XY: 25180 AN XY: 74294

African (AFR) AF: 0.463 AC: 19167 AN: 41442

American (AMR) AF: 0.323 AC: 4933 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1445 AN: 3466

East Asian (EAS) AF: 0.193 AC: 998 AN: 5172

South Asian (SAS) AF: 0.327 AC: 1576 AN: 4818

European-Finnish (FIN) AF: 0.197 AC: 2082 AN: 10556

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21230 AN: 67956

Other (OTH) AF: 0.348 AC: 736 AN: 2112

Alfa AF: 0.332 Hom.: 29200

Bravo AF: 0.361

Asia WGS AF: 0.257 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.69
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1633030; hg19: chr6-29745794;