6-29767327-A-G

Variant names:

• chr6-29767327-A-G
• rs1737049
• ENST00000849873.1:n.421+24780T>C

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+24780T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 149,046 control chromosomes in the GnomAD database, including 9,520 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 (9520 hom., cov: 32)
• Consequence: HLA-F-AS1 ENST00000849873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 16 publications found

Genes affected

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

ENSG00000285761 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000849873.1		n.421+24780T>C		intron	N/A
	HLA-F-AS1	ENST00000849874.1		n.403+24780T>C		intron	N/A
	HLA-F-AS1	ENST00000849875.1		n.354+24780T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 52434 AN: 148944 Hom.: 9512 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.352 AC: 52465 AN: 149046 Hom.: 9520 Cov.: 32 AF XY: 0.345 AC XY: 25157 AN XY: 72900

African (AFR) AF: 0.470 AC: 19200 AN: 40814

American (AMR) AF: 0.334 AC: 4911 AN: 14682

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1447 AN: 3324

East Asian (EAS) AF: 0.198 AC: 1003 AN: 5078

South Asian (SAS) AF: 0.343 AC: 1568 AN: 4574

European-Finnish (FIN) AF: 0.199 AC: 2085 AN: 10476

Middle Eastern (MID) AF: 0.429 AC: 120 AN: 280

European-Non Finnish (NFE) AF: 0.317 AC: 21210 AN: 66846

Other (OTH) AF: 0.356 AC: 735 AN: 2066

Alfa AF: 0.332 Hom.: 9899

Bravo AF: 0.361

Asia WGS AF: 0.280 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.2
DANN	Benign	0.82
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1737049; hg19: chr6-29735104;