6-29740445-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026973.1(HLA-F-AS1):n.150+8455A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,232 control chromosomes in the GnomAD database, including 51,097 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 0.82 (51097 hom., cov: 34)
• Consequence: HLA-F-AS1 NR_026973.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-F-AS1	NR_026973.1	n.150+8455A>G		intron_variant, non_coding_transcript_variant
HLA-F-AS1	NR_026972.1	n.429-1559A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-F-AS1	ENST00000458236.1	n.350-1559A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124226 AN: 152114 Hom.: 51036 Cov.: 34

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.817 AC: 124346 AN: 152232 Hom.: 51097 Cov.: 34 AF XY: 0.815 AC XY: 60633 AN XY: 74408

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.824

Alfa AF: 0.823 Hom.: 34344

Bravo AF: 0.828

Asia WGS AF: 0.939 AC: 3266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.3
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1610603; hg19: chr6-29708222;