2-176183073-T-G

Variant names:

• chr2-176183073-T-G
• rs1446575
• ENST00000417086.6:n.129-3975A>C

Variant summary

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

The ENST00000417086.6(HAGLR):​n.129-3975A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,956 control chromosomes in the GnomAD database, including 21,304 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 0.51 (21304 hom., cov: 32)
• Consequence: HAGLR ENST00000417086.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAGLR	NR_033979.2	n.146-5579A>C		intron_variant	Intron 1 of 2
HAGLR	NR_110459.1	n.155-3975A>C		intron_variant	Intron 1 of 4
HAGLR	NR_110460.1	n.155-3975A>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAGLR	ENST00000417086.6	n.129-3975A>C		intron_variant	Intron 1 of 4	2
HAGLR	ENST00000425005.6	n.134-3975A>C		intron_variant	Intron 1 of 4	3
HAGLR	ENST00000436126.5	n.206-3975A>C		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77265 AN: 151838 Hom.: 21256 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.509 AC: 77369 AN: 151956 Hom.: 21304 Cov.: 32 AF XY: 0.516 AC XY: 38343 AN XY: 74264

African (AFR) AF: 0.685 AC: 28375 AN: 41428

American (AMR) AF: 0.575 AC: 8777 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1186 AN: 3462

East Asian (EAS) AF: 0.742 AC: 3818 AN: 5146

South Asian (SAS) AF: 0.681 AC: 3279 AN: 4818

European-Finnish (FIN) AF: 0.431 AC: 4558 AN: 10566

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25838 AN: 67950

Other (OTH) AF: 0.490 AC: 1033 AN: 2108

Alfa AF: 0.425 Hom.: 60140

Bravo AF: 0.526

Asia WGS AF: 0.700 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1446575; hg19: chr2-177047801;