Variant 7-97858834-GT-GTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

ENSG00000284707 (HGNC:):

ENSG00000284707 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASNS	NM_001673.5 linkuse as main transcript	c.775+19dupA		intron_variant		ENST00000394308.8	NP_001664.3	P08243-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASNS	ENST00000394308.8 linkuse as main transcript	c.775+19dupA		intron_variant		1	NM_001673.5	ENSP00000377845.3		P08243-1

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

GnomAD3 exomes

AF:

0.325

AC:

75984

AN:

233956

Hom.:

13684

AF XY:

0.327

AC XY:

41406

AN XY:

126490

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 SAS exome

AF:

0.442

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

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.459

Gnomad4 ASJ exome

AF:

0.300

Gnomad4 EAS exome

AF:

0.394

Gnomad4 SAS exome

AF:

0.440

Gnomad4 FIN exome

AF:

0.235

Gnomad4 NFE exome

AF:

0.276

Gnomad4 OTH exome

AF:

0.294

GnomAD4 genome

AF:

0.269

AC:

40955

AN:

152008

Hom.:

6067

Cov.:

AF XY:

0.275

AC XY:

20416

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.159

Gnomad4 AMR

AF:

0.412

Gnomad4 ASJ

AF:

0.319

Gnomad4 EAS

AF:

0.416

Gnomad4 SAS

AF:

0.446

Gnomad4 FIN

AF:

0.243

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.284

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

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 15, 2018	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. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jul 15, 2024

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 v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over