Genetic Variant ENST00000417086.6:n.129-3975A>C (chr2-176183073-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.104

Publications

11 publications found

Variant links:

Genes affected

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

HAGLR links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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	Effect	Exon rank
HAGLR	NR_033979.2 link	n.146-5579A>C	intron_variant	Intron 1 of 2
HAGLR	NR_110459.1 link	n.155-3975A>C	intron_variant	Intron 1 of 4
HAGLR	NR_110460.1 link	n.155-3975A>C	intron_variant	Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.509

AC:

77265

AN:

151838

Hom.:

21256

Cov.:

show subpopulations

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.:

AF XY:

0.516

AC XY:

38343

AN XY:

74264

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1812

3624

5437

7249

9061

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.84

PhyloP100

0.10

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over