7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAG

Position:

• chr7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAGGGCGCGGGGCGCAG

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_001673.5(ASNS):​c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000332 in 150,508 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 0.00033 (0 hom., cov: 31)
• Consequence: ASNS NM_001673.5 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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000332 (50/150508) while in subpopulation AFR AF= 0.0011 (44/40082). AF 95% confidence interval is 0.00084. There are 0 homozygotes in gnomad4. There are 23 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASNS	NM_001673.5	c.-60+40_-60+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC		intron_variant		ENST00000394308.8	NP_001664.3
CZ1P-ASNS	NR_147989.1	n.1571-2498_1571-2497insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC		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+41insCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCCCTGCGCCCCGCGCC		intron_variant		1	NM_001673.5	ENSP00000377845	P1

Frequencies

GnomAD3 genomes AF: 0.000332 AC: 50 AN: 150390 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000976

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.000332 AC: 50 AN: 150508 Hom.: 0 Cov.: 31 AF XY: 0.000313 AC XY: 23 AN XY: 73592

Gnomad4 AFR AF: 0.00110

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000978

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

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;