ENST00000849873.1:n.421+14000C>T

Variant names:

• chr6-29778107-G-A
• rs1614309
• ENST00000849873.1:n.421+14000C>T

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+14000C>T 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 152,082 control chromosomes in the GnomAD database, including 9,529 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 (9529 hom., cov: 32)
• Consequence: HLA-F-AS1 ENST00000849873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 18 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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	ENST00000849873.1	n.421+14000C>T		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849874.1	n.403+14000C>T		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849875.1	n.354+14000C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52461 AN: 151964 Hom.: 9521 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: 0.194

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: 52491 AN: 152082 Hom.: 9529 Cov.: 32 AF XY: 0.339 AC XY: 25189 AN XY: 74342

African (AFR) AF: 0.463 AC: 19176 AN: 41446

American (AMR) AF: 0.323 AC: 4929 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1449 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1006 AN: 5182

South Asian (SAS) AF: 0.327 AC: 1579 AN: 4828

European-Finnish (FIN) AF: 0.197 AC: 2088 AN: 10576

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

European-Non Finnish (NFE) AF: 0.312 AC: 21221 AN: 67980

Other (OTH) AF: 0.349 AC: 736 AN: 2110

Alfa AF: 0.324 Hom.: 7176

Bravo AF: 0.361

Asia WGS AF: 0.257 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.47
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1614309; hg19: chr6-29745884;