rs2513077

Positions:

• chr11-62338453-G-A
• chr11-62338453-G-C
• chr11-62338453-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001083926.2(ASRGL1):​c.190+286G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 340,808 control chromosomes in the GnomAD database, including 129,675 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.85 (55254 hom., cov: 31)
  • Exomes 𝑓: 0.89 (74421 hom.)
• Consequence: ASRGL1 NM_001083926.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASRGL1	NM_001083926.2	c.190+286G>A		intron_variant		ENST00000415229.6	NP_001077395.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASRGL1	ENST00000415229.6	c.190+286G>A		intron_variant		1	NM_001083926.2	ENSP00000400057	P1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128978 AN: 152086 Hom.: 55231 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.860

GnomAD4 exome AF: 0.887 AC: 167383 AN: 188604 Hom.: 74421 AF XY: 0.888 AC XY: 85735 AN XY: 96598

Gnomad4 AFR exome AF: 0.716

Gnomad4 AMR exome AF: 0.920

Gnomad4 ASJ exome AF: 0.875

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.911

Gnomad4 FIN exome AF: 0.923

Gnomad4 NFE exome AF: 0.877

Gnomad4 OTH exome AF: 0.878

GnomAD4 genome AF: 0.848 AC: 129053 AN: 152204 Hom.: 55254 Cov.: 31 AF XY: 0.852 AC XY: 63440 AN XY: 74432

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.861

Alfa AF: 0.856 Hom.: 5316

Bravo AF: 0.840

Asia WGS AF: 0.952 AC: 3310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2513077; hg19: chr11-62105925;