7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAG

Position:

• chr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000394308.8(ASNS):​c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00323 in 151,450 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0032 (2 hom., cov: 31)
  • Exomes 𝑓: 0.0043 (1 hom.)
• Consequence: ASNS ENST00000394308.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

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 Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00322 (485/150510) while in subpopulation AFR AF= 0.00776 (311/40084). AF 95% confidence interval is 0.00705. There are 2 homozygotes in gnomad4. There are 244 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASNS	NM_001673.5	c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCC		intron_variant		ENST00000394308.8	NP_001664.3
CZ1P-ASNS	NR_147989.1	n.1571-2498_1571-2497insCTGCGCCCCGCGCCCTGCGCCCCGCGCC		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASNS	ENST00000394308.8	c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCC		intron_variant		1	NM_001673.5	ENSP00000377845	P1

Frequencies

GnomAD3 genomes AF: 0.00323 AC: 486 AN: 150392 Hom.: 3 Cov.: 31

Gnomad AFR AF: 0.00776

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00375

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.00781

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.000754

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000795

Gnomad OTH AF: 0.00338

GnomAD4 exome AF: 0.00426 AC: 4 AN: 940 Hom.: 1 Cov.: 0 AF XY: 0.00142 AC XY: 1 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: 0.0250

Gnomad4 SAS exome AF: 0.0833

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00125

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00322 AC: 485 AN: 150510 Hom.: 2 Cov.: 31 AF XY: 0.00332 AC XY: 244 AN XY: 73594

Gnomad4 AFR AF: 0.00776

Gnomad4 AMR AF: 0.00374

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.00744

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.000754

Gnomad4 NFE AF: 0.000795

Gnomad4 OTH AF: 0.00334

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;