rs1737060

Variant names:

• chr6-29765192-G-C
• rs1737060

Your query was ambiguous. Multiple possible variants found:

• chr6-29765192-G-C
• chr6-29765192-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.791 in 152,096 control chromosomes in the GnomAD database, including 47,850 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 0.79 (47850 hom., cov: 32)
• Consequence: LOC353010 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 23 publications found

Genes affected

LOC353010 (HGNC:):

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-F-AS1	ENST00000849873.1		n.421+26915C>G		intron	N/A
	HLA-F-AS1	ENST00000849874.1		n.403+26915C>G		intron	N/A
	HLA-F-AS1	ENST00000849875.1		n.354+26915C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120192 AN: 151978 Hom.: 47796 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.791 AC: 120306 AN: 152096 Hom.: 47850 Cov.: 32 AF XY: 0.789 AC XY: 58635 AN XY: 74336

African (AFR) AF: 0.721 AC: 29903 AN: 41448

American (AMR) AF: 0.856 AC: 13086 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4672 AN: 5186

South Asian (SAS) AF: 0.873 AC: 4202 AN: 4814

European-Finnish (FIN) AF: 0.689 AC: 7276 AN: 10558

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55438 AN: 68004

Other (OTH) AF: 0.803 AC: 1698 AN: 2114

Alfa AF: 0.801 Hom.: 6080

Bravo AF: 0.800

Asia WGS AF: 0.877 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.21
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs1737060; hg19: chr6-29732969;