rs9258260

Variant names:

• chr6-29755384-C-T
• rs9258260
• ENST00000648999.2:n.355+2457C>T

Variant summary

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

The ENST00000648999.2(ENSG00000285761):​n.355+2457C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,222 control chromosomes in the GnomAD database, including 1,240 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 0.12 (1240 hom., cov: 33)
• Consequence: ENSG00000285761 ENST00000648999.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 29 publications found

Genes affected

ENSG00000285761 (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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648999.2. 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
	ENSG00000285761	ENST00000648999.2		n.355+2457C>T		intron	N/A
	HLA-F-AS1	ENST00000849873.1		n.422-28245G>A		intron	N/A
	HLA-F-AS1	ENST00000849874.1		n.404-28145G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17705 AN: 152104 Hom.: 1236 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0937

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.116 AC: 17722 AN: 152222 Hom.: 1240 Cov.: 33 AF XY: 0.117 AC XY: 8743 AN XY: 74442

African (AFR) AF: 0.141 AC: 5840 AN: 41530

American (AMR) AF: 0.0912 AC: 1395 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1469 AN: 5168

South Asian (SAS) AF: 0.242 AC: 1168 AN: 4824

European-Finnish (FIN) AF: 0.0600 AC: 637 AN: 10608

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0937 AC: 6372 AN: 68012

Other (OTH) AF: 0.120 AC: 254 AN: 2108

Alfa AF: 0.102 Hom.: 3055

Bravo AF: 0.119

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.95
DANN	Benign	0.61
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs9258260; hg19: chr6-29723161;