6-29761509-C-T

Variant names:

• chr6-29761509-C-T
• rs1610630
• ENST00000648999.2:n.356-265C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000648999.2(ENSG00000285761):​n.356-265C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,200 control chromosomes in the GnomAD database, including 51,041 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 0.82 (51041 hom., cov: 32)
• Consequence: ENSG00000285761 ENST00000648999.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 8 publications found

Genes affected

ENSG00000285761 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285761	ENST00000648999.2	n.356-265C>T		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849873.1	n.421+30598G>A		intron_variant	Intron 1 of 1
HLA-F-AS1	ENST00000849874.1	n.403+30598G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124152 AN: 152082 Hom.: 50980 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.817 AC: 124272 AN: 152200 Hom.: 51041 Cov.: 32 AF XY: 0.815 AC XY: 60620 AN XY: 74420

African (AFR) AF: 0.788 AC: 32724 AN: 41516

American (AMR) AF: 0.866 AC: 13260 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3035 AN: 3472

East Asian (EAS) AF: 0.983 AC: 5104 AN: 5190

South Asian (SAS) AF: 0.928 AC: 4488 AN: 4834

European-Finnish (FIN) AF: 0.690 AC: 7289 AN: 10560

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55609 AN: 68004

Other (OTH) AF: 0.825 AC: 1744 AN: 2114

Alfa AF: 0.826 Hom.: 24881

Bravo AF: 0.827

Asia WGS AF: 0.939 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	2.3
DANN	Benign	0.89
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1610630; hg19: chr6-29729286;