rs1737010

Variant names:

• chr6-29789223-A-C
• rs1737010
• ENST00000849873.1:n.421+2884T>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+2884T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 152,006 control chromosomes in the GnomAD database, including 13,500 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 0.41 (13500 hom., cov: 31)
• Consequence: HLA-F-AS1 ENST00000849873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 8 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 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+2884T>G		intron	N/A
	HLA-F-AS1	ENST00000849874.1		n.403+2884T>G		intron	N/A
	HLA-F-AS1	ENST00000849875.1		n.354+2884T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61534 AN: 151886 Hom.: 13478 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.405 AC: 61595 AN: 152006 Hom.: 13500 Cov.: 31 AF XY: 0.396 AC XY: 29444 AN XY: 74304

African (AFR) AF: 0.569 AC: 23571 AN: 41438

American (AMR) AF: 0.415 AC: 6339 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1032 AN: 5152

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4816

European-Finnish (FIN) AF: 0.207 AC: 2188 AN: 10572

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23801 AN: 67964

Other (OTH) AF: 0.423 AC: 892 AN: 2110

Alfa AF: 0.370 Hom.: 4176

Bravo AF: 0.431

Asia WGS AF: 0.288 AC: 1005 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	1.3
DANN	Benign	0.49
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1737010; hg19: chr6-29757000;