chr2-176177905-A-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000416928.9(HAGLR):​n.269T>A 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 0.0000236 in 169,408 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000020 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000058 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAGLR	NR_110458.1		n.225T>A		non_coding_transcript_exon	Exon 1 of 3
	HAGLR	NR_110462.1		n.225T>A		non_coding_transcript_exon	Exon 1 of 2
	HAGLR	NR_033979.2		n.146-411T>A		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0000197 AC: 3 AN: 152032 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000576 AC: 1 AN: 17376 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 9184

African (AFR) AF: 0.00 AC: 0 AN: 346

American (AMR) AF: 0.00 AC: 0 AN: 386

Ashkenazi Jewish (ASJ) AF: 0.00189 AC: 1 AN: 528

East Asian (EAS) AF: 0.00 AC: 0 AN: 1986

South Asian (SAS) AF: 0.00 AC: 0 AN: 122

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2070

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 104

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10858

Other (OTH) AF: 0.00 AC: 0 AN: 976

GnomAD4 genome AF: 0.0000197 AC: 3 AN: 152032 Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3 AN XY: 74226

African (AFR) AF: 0.0000483 AC: 2 AN: 41414

American (AMR) AF: 0.00 AC: 0 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5158

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 67994

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 135094

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2072590;

hg19: chr2-177042633;