rs36021744

chr7-97858834-GT-Gchr7-97858834-GT-GTTchr7-97858834-GT-GTTTchr7-97858834-GT-GTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001673.5(ASNS):c.775+19del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000542 in 1,587,198 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.000086 (0 hom., cov: 21)
  • Exomes 𝑓: 0.000051 (0 hom.)
• Consequence: ASNS NM_001673.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0440

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 7-97858834-GT-G is Benign according to our data. Variant chr7-97858834-GT-G is described in ClinVar as [Benign]. Clinvar id is 1600985.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-97858834-GT-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASNS	NM_001673.5	c.775+19del		intron_variant		ENST00000394308.8
CZ1P-ASNS	NR_147989.1	n.2404+19del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ASNS	ENST00000394308.8	c.775+19del		intron_variant		1	NM_001673.5	P1

Frequencies

GnomAD3 genomes AF: 0.0000856 AC: 13 AN: 151950 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.0000725

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.0000898 AC: 21 AN: 233956 Hom.: 0 AF XY: 0.0000870 AC XY: 11 AN XY: 126490

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000371

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000644

Gnomad OTH exome AF: 0.000532

GnomAD4 exome AF: 0.0000509 AC: 73 AN: 1435248 Hom.: 0 Cov.: 30 AF XY: 0.0000476 AC XY: 34 AN XY: 714364

Gnomad4 AFR exome AF: 0.0000311

Gnomad4 AMR exome AF: 0.000356

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000122

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000391

Gnomad4 OTH exome AF: 0.000135

GnomAD4 genome AF: 0.0000856 AC: 13 AN: 151950 Hom.: 0 Cov.: 21 AF XY: 0.0000809 AC XY: 6 AN XY: 74208

Gnomad4 AFR AF: 0.0000725

Gnomad4 AMR AF: 0.000589

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.000479

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 24, 2024

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs36021744; hg19: chr7-97488146;