rs2072590

Positions:

• chr2-176177905-A-C
• chr2-176177905-A-T

Variant summary

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

The ENST00000416928.8(HAGLR):​n.234T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 169,404 control chromosomes in the GnomAD database, including 48,939 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 0.76 (44767 hom., cov: 32)
  • Exomes 𝑓: 0.69 (4172 hom.)
• Consequence: HAGLR ENST00000416928.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

Genes affected

HAGLR (HGNC:43755): (HOXD antisense growth-associated long non-coding RNA)

HAGLROS (HGNC:50646): (HAGLR opposite strand lncRNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HAGLR	NR_033979.2	n.146-411T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAGLROS	ENST00000426615.4	n.189A>C		non_coding_transcript_exon_variant	1/2	2
HAGLR	ENST00000452365.2	n.184-49T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115710 AN: 151998 Hom.: 44711 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.764

GnomAD4 exome AF: 0.694 AC: 11990 AN: 17288 Hom.: 4172 Cov.: 0 AF XY: 0.691 AC XY: 6316 AN XY: 9134

Gnomad4 AFR exome AF: 0.849

Gnomad4 AMR exome AF: 0.818

Gnomad4 ASJ exome AF: 0.676

Gnomad4 EAS exome AF: 0.784

Gnomad4 SAS exome AF: 0.852

Gnomad4 FIN exome AF: 0.684

Gnomad4 NFE exome AF: 0.664

Gnomad4 OTH exome AF: 0.731

GnomAD4 genome AF: 0.761 AC: 115820 AN: 152116 Hom.: 44767 Cov.: 32 AF XY: 0.764 AC XY: 56820 AN XY: 74332

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.763

Alfa AF: 0.695 Hom.: 57252

Bravo AF: 0.772

Asia WGS AF: 0.796 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
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: rs2072590; hg19: chr2-177042633;