Genetic Variant NM_001673.5:c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC (chr7-97872310-T-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001673.5(ASNS):c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0014 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0011 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ASNS
NM_001673.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.809

Publications

8 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:

ENSG00000297732 (HGNC:):

ENSG00000297732 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC	intron	N/A	NP_001664.3
ASNS	NM_001352496.2		c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC	intron	N/A	NP_001339425.1
ASNS	NM_183356.4		c.-338+40_-338+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC	intron	N/A	NP_899199.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ASNS	ENST00000394308.8	TSL:1 MANE Select	c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC	intron	N/A	ENSP00000377845.3
ASNS	ENST00000175506.8	TSL:1	c.-338+40_-338+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC	intron	N/A	ENSP00000175506.4
ENSG00000297732	ENST00000750621.1		n.123_124insGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGC	non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.00138

AC:

208

AN:

150392

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00433

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000460

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00234

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000118

Gnomad OTH

AF:

0.00241

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00106

AC:

AN:

940

Hom.:

Cov.:

AF XY:

0.00142

AC XY:

AN XY:

706

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00125

AC:

AN:

798

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00138

AC:

208

AN:

150510

Hom.:

Cov.:

AF XY:

0.00145

AC XY:

107

AN XY:

73594

show subpopulations

African (AFR)

AF:

0.00432

AC:

173

AN:

40084

American (AMR)

AF:

0.000460

AC:

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3460

East Asian (EAS)

AF:

0.00235

AC:

AN:

5110

South Asian (SAS)

AF:

0.000622

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000118

AC:

AN:

67904

Other (OTH)

AF:

0.00239

AC:

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.81

Mutation Taster

=100/0

polymorphism

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over