Genetic Variant NM_001083926.2:c.190+286G>A (chr11-62338453-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001083926.2(ASRGL1):c.190+286G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 340,808 control chromosomes in the GnomAD database, including 129,675 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 0.85 ( 55254 hom., cov: 31)

Exomes 𝑓: 0.89 ( 74421 hom. )

Consequence

ASRGL1
NM_001083926.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.61

Publications

11 publications found

Variant links:

Genes affected

ASRGL1 (HGNC:16448): (asparaginase and isoaspartyl peptidase 1) Enables asparaginase activity and beta-aspartyl-peptidase activity. Involved in asparagine catabolic process via L-aspartate. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ASRGL1 Gene-Disease associations (from GenCC):

inherited retinal dystrophy
Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

ASRGL1 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=-1.02).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001083926.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ASRGL1	NM_001083926.2	MANE Select	c.190+286G>A	intron	N/A	NP_001077395.1	A0A024R573
ASRGL1	NM_025080.4		c.190+286G>A	intron	N/A	NP_079356.3
ASRGL1	NM_001441216.1		c.190+286G>A	intron	N/A	NP_001428145.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ASRGL1	ENST00000415229.6	TSL:1 MANE Select	c.190+286G>A	intron	N/A	ENSP00000400057.2	Q7L266-1
ASRGL1	ENST00000301776.9	TSL:1	c.190+286G>A	intron	N/A	ENSP00000301776.5	Q7L266-1
ASRGL1	ENST00000628829.2	TSL:1	c.190+286G>A	intron	N/A	ENSP00000486943.1	E9PJK6

Frequencies

GnomAD3 genomes

AF:

0.848

AC:

128978

AN:

152086

Hom.:

55231

Cov.:

show subpopulations

Gnomad AFR

AF:

0.718

Gnomad AMI

AF:

0.901

Gnomad AMR

AF:

0.905

Gnomad ASJ

AF:

0.880

Gnomad EAS

AF:

0.998

Gnomad SAS

AF:

0.933

Gnomad FIN

AF:

0.934

Gnomad MID

AF:

0.892

Gnomad NFE

AF:

0.881

Gnomad OTH

AF:

0.860

GnomAD4 exome

AF:

0.887

AC:

167383

AN:

188604

Hom.:

74421

AF XY:

0.888

AC XY:

85735

AN XY:

96598

show subpopulations

African (AFR)

AF:

0.716

AC:

3936

AN:

5498

American (AMR)

AF:

0.920

AC:

6780

AN:

7366

Ashkenazi Jewish (ASJ)

AF:

0.875

AC:

6282

AN:

7178

East Asian (EAS)

AF:

1.00

AC:

14471

AN:

14476

South Asian (SAS)

AF:

0.911

AC:

8062

AN:

8854

European-Finnish (FIN)

AF:

0.923

AC:

10579

AN:

11460

Middle Eastern (MID)

AF:

0.820

AC:

795

AN:

970

European-Non Finnish (NFE)

AF:

0.877

AC:

105716

AN:

120544

Other (OTH)

AF:

0.878

AC:

10762

AN:

12258

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

894

1788

2681

3575

4469

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

444

888

1332

1776

2220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.848

AC:

129053

AN:

152204

Hom.:

55254

Cov.:

AF XY:

0.852

AC XY:

63440

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.718

AC:

29768

AN:

41472

American (AMR)

AF:

0.905

AC:

13837

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.880

AC:

3056

AN:

3472

East Asian (EAS)

AF:

0.998

AC:

5177

AN:

5186

South Asian (SAS)

AF:

0.932

AC:

4499

AN:

4826

European-Finnish (FIN)

AF:

0.934

AC:

9913

AN:

10610

Middle Eastern (MID)

AF:

0.898

AC:

264

AN:

294

European-Non Finnish (NFE)

AF:

0.881

AC:

59902

AN:

68030

Other (OTH)

AF:

0.861

AC:

1815

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

964

1928

2892

3856

4820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<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:

0.850

Hom.:

5519

Bravo

AF:

0.840

Asia WGS

AF:

0.952

AC:

3310

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.12

(source)

DANN

Benign

0.18

PhyloP100

-1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over