rs12073837

Positions:

• chr1-220836863-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046901.1(HLX-AS1):​n.293-3671G>A variant causes a intron, non coding transcript 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: HLX-AS1 NR_046901.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.725

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
HLX-AS1	NR_046901.1	n.293-3671G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLX-AS1	ENST00000552026.1	n.293-3671G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.230

Alfa AF: 0.264 Hom.: 12347

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

Splicing

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

Publications

LitVar

Other links and lift over

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