chr7-97858834-G-GT

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001673.5(ASNS):c.775+19dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,586,306 control chromosomes in the GnomAD database, including 70,537 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6067 hom., cov: 21)

Exomes 𝑓: 0.29 ( 64470 hom. )

Consequence

ASNS
NM_001673.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0440

Publications

2 publications found

Variant links:

Genes affected

ASNS (HGNC:753): (asparagine synthetase (glutamine-hydrolyzing)) The protein encoded by this gene is involved in the synthesis of asparagine. This gene complements a mutation in the temperature-sensitive hamster mutant ts11, which blocks progression through the G1 phase of the cell cycle at nonpermissive temperature. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, May 2010]

ASNS Gene-Disease associations (from GenCC):

congenital microcephaly - severe encephalopathy - progressive cerebral atrophy syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen

ASNS links:

ENSG00000284707 (HGNC:):

ENSG00000284707 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 7-97858834-G-GT is Benign according to our data. Variant chr7-97858834-G-GT is described in ClinVar as Benign. ClinVar VariationId is 680024.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001673.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ASNS	NM_001673.5	MANE Select	c.775+19dupA	intron	N/A	NP_001664.3
ASNS	NM_001352496.2		c.775+19dupA	intron	N/A	NP_001339425.1
ASNS	NM_133436.3		c.775+19dupA	intron	N/A	NP_597680.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ASNS	ENST00000394308.8	TSL:1 MANE Select	c.775+19_775+20insA	intron	N/A	ENSP00000377845.3
ASNS	ENST00000175506.8	TSL:1	c.775+19_775+20insA	intron	N/A	ENSP00000175506.4
ASNS	ENST00000394309.7	TSL:2	c.775+19_775+20insA	intron	N/A	ENSP00000377846.3

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

40951

AN:

151890

Hom.:

6072

Cov.:

show subpopulations

Gnomad AFR

AF:

0.159

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.411

Gnomad ASJ

AF:

0.319

Gnomad EAS

AF:

0.417

Gnomad SAS

AF:

0.446

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.286

GnomAD2 exomes

AF:

0.325

AC:

75984

AN:

233956

AF XY:

0.327

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.471

Gnomad ASJ exome

AF:

0.293

Gnomad EAS exome

AF:

0.422

Gnomad FIN exome

AF:

0.229

Gnomad NFE exome

AF:

0.287

Gnomad OTH exome

AF:

0.316

GnomAD4 exome

AF:

0.291

AC:

417543

AN:

1434298

Hom.:

64470

Cov.:

AF XY:

0.295

AC XY:

210420

AN XY:

713892

show subpopulations

African (AFR)

AF:

0.154

AC:

4953

AN:

32138

American (AMR)

AF:

0.459

AC:

18053

AN:

39294

Ashkenazi Jewish (ASJ)

AF:

0.300

AC:

7559

AN:

25226

East Asian (EAS)

AF:

0.394

AC:

15551

AN:

39458

South Asian (SAS)

AF:

0.440

AC:

36097

AN:

82052

European-Finnish (FIN)

AF:

0.235

AC:

12448

AN:

53076

Middle Eastern (MID)

AF:

0.351

AC:

1968

AN:

5602

European-Non Finnish (NFE)

AF:

0.276

AC:

303471

AN:

1098156

Other (OTH)

AF:

0.294

AC:

17443

AN:

59296

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

14222

28444

42665

56887

71109

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10214

20428

30642

40856

51070

<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:

0.269

AC:

40955

AN:

152008

Hom.:

6067

Cov.:

AF XY:

0.275

AC XY:

20416

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.159

AC:

6585

AN:

41462

American (AMR)

AF:

0.412

AC:

6289

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.319

AC:

1105

AN:

3464

East Asian (EAS)

AF:

0.416

AC:

2149

AN:

5160

South Asian (SAS)

AF:

0.446

AC:

2143

AN:

4808

European-Finnish (FIN)

AF:

0.243

AC:

2568

AN:

10548

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.283

AC:

19218

AN:

67968

Other (OTH)

AF:

0.284

AC:

599

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1471

2942

4414

5885

7356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

434

868

1302

1736

2170

<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:

0.200

Hom.:

663

Bravo

AF:

0.274

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 15, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not specified

Benign:1

Jul 15, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 72% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 67. Only high quality variants are reported.

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.044

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over