chr1-220836863-C-T

Variant names:

• chr1-220836863-C-T
• rs12073837
• ENST00000651706.1:n.842+31589C>T

Variant summary

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

The ENST00000651706.1(ENSG00000286231):​n.842+31589C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,940 control chromosomes in the GnomAD database, including 4,672 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 0.24 (4672 hom., cov: 32)
• Consequence: ENSG00000286231 ENST00000651706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLX-AS1	NR_046901.1	n.293-3671G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286231	ENST00000651706.1	n.842+31589C>T		intron_variant	Intron 6 of 8			ENSP00000499157.1
HLX-AS1	ENST00000552026.1	n.293-3671G>A		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36100 AN: 151822 Hom.: 4666 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.238 AC: 36124 AN: 151940 Hom.: 4672 Cov.: 32 AF XY: 0.242 AC XY: 17990 AN XY: 74252

African (AFR) AF: 0.133 AC: 5512 AN: 41490

American (AMR) AF: 0.278 AC: 4236 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3466

East Asian (EAS) AF: 0.289 AC: 1493 AN: 5158

South Asian (SAS) AF: 0.271 AC: 1304 AN: 4806

European-Finnish (FIN) AF: 0.328 AC: 3453 AN: 10514

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18544 AN: 67956

Other (OTH) AF: 0.230 AC: 485 AN: 2112

Alfa AF: 0.261 Hom.: 24888

Bravo AF: 0.232

Asia WGS AF: 0.247 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.79
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs12073837; hg19: chr1-221010205; COSMIC: COSV70801691;