chr1-220879115-C-G

Variant names:

• chr1-220879115-C-G
• rs2184658
• ENST00000651706.1:n.843-2079C>G

Variant summary

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

The ENST00000651706.1(ENSG00000286231):​n.843-2079C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,226 control chromosomes in the GnomAD database, including 3,283 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 0.20 (3283 hom., cov: 33)
• Consequence: ENSG00000286231 ENST00000651706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651706.1. 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
	HLX-AS1	NR_046901.1		n.292+734G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286231	ENST00000651706.1		n.843-2079C>G		intron	N/A	ENSP00000499157.1
	HLX-AS1	ENST00000691443.2		n.163G>C		non_coding_transcript_exon	Exon 1 of 1
	HLX-AS1	ENST00000552026.1	TSL:4	n.292+734G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30818 AN: 152108 Hom.: 3280 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0894

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.203 AC: 30834 AN: 152226 Hom.: 3283 Cov.: 33 AF XY: 0.201 AC XY: 14979 AN XY: 74416

African (AFR) AF: 0.240 AC: 9992 AN: 41548

American (AMR) AF: 0.166 AC: 2538 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3470

East Asian (EAS) AF: 0.0890 AC: 460 AN: 5166

South Asian (SAS) AF: 0.190 AC: 917 AN: 4830

European-Finnish (FIN) AF: 0.257 AC: 2725 AN: 10588

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.187 AC: 12734 AN: 68002

Other (OTH) AF: 0.175 AC: 371 AN: 2116

Alfa AF: 0.112 Hom.: 181

Bravo AF: 0.195

Asia WGS AF: 0.159 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.71
DANN	Benign	0.58
PhyloP100		-1.5
PromoterAI		-0.041	Neutral
Mutation Taster		=299/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2184658; hg19: chr1-221052457;