NM_001083926.2:c.97dupG

Variant names:

• chr11-62338073-C-CG
• rs2134556258
• NM_001083926.2:c.97dupG

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001083926.2(ASRGL1):​c.97dupG​(p.Val33GlyfsTer42) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. V33V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 34)
• Consequence: ASRGL1 NM_001083926.2 frameshift
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.278
• Publications: 0 publications found

Genes affected

ASRGL1 (HGNC:16448): (asparaginase and isoaspartyl peptidase 1) Enables asparaginase activity and beta-aspartyl-peptidase activity. Involved in asparagine catabolic process via L-aspartate. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ASRGL1 Gene-Disease associations (from GenCC):

• inherited retinal dystrophy

  Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

ENSG00000255118 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001083926.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASRGL1	NM_001083926.2	MANE Select	c.97dupG	p.Val33GlyfsTer42	frameshift	Exon 2 of 7	NP_001077395.1	A0A024R573
	ASRGL1	NM_025080.4		c.97dupG	p.Val33GlyfsTer42	frameshift	Exon 2 of 7	NP_079356.3
	ASRGL1	NM_001441216.1		c.97dupG	p.Val33GlyfsTer42	frameshift	Exon 2 of 5	NP_001428145.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASRGL1	ENST00000415229.6	TSL:1 MANE Select	c.97dupG	p.Val33GlyfsTer42	frameshift	Exon 2 of 7	ENSP00000400057.2	Q7L266-1
	ASRGL1	ENST00000301776.9	TSL:1	c.97dupG	p.Val33GlyfsTer42	frameshift	Exon 2 of 7	ENSP00000301776.5	Q7L266-1
	ASRGL1	ENST00000628829.2	TSL:1	c.97dupG	p.Val33GlyfsTer38	frameshift	Exon 2 of 6	ENSP00000486943.1	E9PJK6

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 34

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.28

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

Other links and lift over

dbSNP: rs2134556258; hg19: chr11-62105545;