6-29821394-T-C

Variant names:

• chr6-29821394-T-C
• rs1610677
• ENST00000849927.1:n.26+7077A>G

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.26+7077A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,584 control chromosomes in the GnomAD database, including 17,946 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 0.48 (17946 hom., cov: 31)
• Consequence: HLA-F-AS1 ENST00000849927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 26 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=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849927.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000849927.1		n.26+7077A>G		intron	N/A
	HLA-F-AS1	ENST00000849935.1		n.230+6326A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73307 AN: 151466 Hom.: 17923 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.484 AC: 73370 AN: 151584 Hom.: 17946 Cov.: 31 AF XY: 0.484 AC XY: 35850 AN XY: 74070

African (AFR) AF: 0.509 AC: 21049 AN: 41318

American (AMR) AF: 0.513 AC: 7812 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1960 AN: 3460

East Asian (EAS) AF: 0.606 AC: 3106 AN: 5124

South Asian (SAS) AF: 0.665 AC: 3195 AN: 4808

European-Finnish (FIN) AF: 0.338 AC: 3562 AN: 10526

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31043 AN: 67838

Other (OTH) AF: 0.505 AC: 1057 AN: 2094

Alfa AF: 0.482 Hom.: 46187

Bravo AF: 0.496

Asia WGS AF: 0.682 AC: 2371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.29
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1610677; hg19: chr6-29789171;