2-176177905-A-C

Variant names:

• chr2-176177905-A-C
• rs2072590
• ENST00000416928.9:n.269T>G

Variant summary

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

The ENST00000416928.9(HAGLR):​n.269T>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 ENST00000416928.9 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 64 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416928.9. 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
	HAGLR	NR_110458.1		n.225T>G		non_coding_transcript_exon	Exon 1 of 3
	HAGLR	NR_110462.1		n.225T>G		non_coding_transcript_exon	Exon 1 of 2
	HAGLR	NR_033979.2		n.146-411T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAGLR	ENST00000416928.9	TSL:1	n.269T>G		non_coding_transcript_exon	Exon 1 of 3
	HAGLROS	ENST00000426615.5	TSL:2	n.189A>C		non_coding_transcript_exon	Exon 1 of 2
	HAGLR	ENST00000456876.2	TSL:2	n.244T>G		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AF: 0.849 AC: 292 AN: 344

American (AMR) AF: 0.818 AC: 311 AN: 380

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 353 AN: 522

East Asian (EAS) AF: 0.784 AC: 1552 AN: 1980

South Asian (SAS) AF: 0.852 AC: 104 AN: 122

European-Finnish (FIN) AF: 0.684 AC: 1402 AN: 2050

Middle Eastern (MID) AF: 0.769 AC: 80 AN: 104

European-Non Finnish (NFE) AF: 0.664 AC: 7187 AN: 10816

Other (OTH) AF: 0.731 AC: 709 AN: 970

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

African (AFR) AF: 0.889 AC: 36922 AN: 41526

American (AMR) AF: 0.788 AC: 12048 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2441 AN: 3470

East Asian (EAS) AF: 0.761 AC: 3913 AN: 5144

South Asian (SAS) AF: 0.846 AC: 4074 AN: 4816

European-Finnish (FIN) AF: 0.712 AC: 7528 AN: 10574

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46393 AN: 67974

Other (OTH) AF: 0.763 AC: 1613 AN: 2114

Alfa AF: 0.705 Hom.: 135094

Bravo AF: 0.772

Asia WGS AF: 0.796 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2072590; hg19: chr2-177042633;