ENST00000651706.1:n.843-26028T>C

Variant names:

• chr1-220855166-T-C
• rs11118620
• ENST00000651706.1:n.843-26028T>C

Variant summary

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

The ENST00000651706.1(ENSG00000286231):​n.843-26028T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,054 control chromosomes in the GnomAD database, including 6,365 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 0.28 (6365 hom., cov: 32)
• Consequence: ENSG00000286231 ENST00000651706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 14 publications found

Genes affected

ENSG00000286231 (HGNC:):

HLX-AS1 (HGNC:42509): (HLX antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLX-AS1	NR_046901.1	n.293-21974A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286231	ENST00000651706.1	n.843-26028T>C		intron_variant	Intron 6 of 8			ENSP00000499157.1
HLX-AS1	ENST00000552026.1	n.293-21974A>G		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43268 AN: 151936 Hom.: 6365 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.285 AC: 43278 AN: 152054 Hom.: 6365 Cov.: 32 AF XY: 0.287 AC XY: 21353 AN XY: 74320

African (AFR) AF: 0.234 AC: 9716 AN: 41470

American (AMR) AF: 0.371 AC: 5663 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 754 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2201 AN: 5166

South Asian (SAS) AF: 0.360 AC: 1735 AN: 4820

European-Finnish (FIN) AF: 0.265 AC: 2799 AN: 10568

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19480 AN: 67976

Other (OTH) AF: 0.310 AC: 653 AN: 2108

Alfa AF: 0.235 Hom.: 1273

Bravo AF: 0.290

Asia WGS AF: 0.372 AC: 1291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.60
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs11118620; hg19: chr1-221028508;