rs3832526

chr7-97872310-TGGCGCGGGGCGCAG-Tchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCACGGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGchr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCGGGGCGCAG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001673.5(ASNS):c.-60+27_-60+40del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 150,392 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ASNS NM_001673.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

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]

CZ1P-ASNS (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASNS	NM_001673.5	c.-60+27_-60+40del		intron_variant		ENST00000394308.8
CZ1P-ASNS	NR_147989.1	n.1571-2511_1571-2498del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASNS	ENST00000394308.8	c.-60+27_-60+40del		intron_variant		1	NM_001673.5	P1

Frequencies

GnomAD3 genomes AF: 0.0000199 AC: 3 AN: 150392 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 940 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 706

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000199 AC: 3 AN: 150392 Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1 AN XY: 73464

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3832526; hg19: chr7-97501622;