Variant 11-62337969-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The ENST00000301776.9(ASRGL1):c.-9T>C variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 1,586,362 control chromosomes in the GnomAD database, including 64,524 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.27 ( 5786 hom., cov: 34)

Exomes 𝑓: 0.28 ( 58738 hom. )

Consequence

ASRGL1
ENST00000301776.9 splice_region, 5_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.147

Variant links:

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 links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 11-62337969-T-C is Benign according to our data. Variant chr11-62337969-T-C is described in ClinVar as [Benign]. Clinvar id is 3059422.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ASRGL1	NM_001083926.2 linkuse as main transcript	c.-9T>C		5_prime_UTR_variant	2/7	ENST00000415229.6	NP_001077395.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ASRGL1	ENST00000415229.6 linkuse as main transcript	c.-9T>C		5_prime_UTR_variant	2/7	1	NM_001083926.2	ENSP00000400057	P1	Q7L266-1
	ENST00000400902.4 linkuse as main transcript	n.122A>G		non_coding_transcript_exon_variant	1/2	4

Frequencies

GnomAD3 genomes

AF:

0.273

AC:

41553

AN:

152124

Hom.:

5779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.307

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.262

GnomAD3 exomes

AF:

0.292

AC:

60025

AN:

205536

Hom.:

8979

AF XY:

0.292

AC XY:

32340

AN XY:

110818

show subpopulations

Gnomad AFR exome

AF:

0.250

Gnomad AMR exome

AF:

0.352

Gnomad ASJ exome

AF:

0.204

Gnomad EAS exome

AF:

0.286

Gnomad SAS exome

AF:

0.353

Gnomad FIN exome

AF:

0.304

Gnomad NFE exome

AF:

0.269

Gnomad OTH exome

AF:

0.265

GnomAD4 exome

AF:

0.284

AC:

406900

AN:

1434122

Hom.:

58738

Cov.:

AF XY:

0.285

AC XY:

202702

AN XY:

710694

show subpopulations

Gnomad4 AFR exome

AF:

0.250

Gnomad4 AMR exome

AF:

0.346

Gnomad4 ASJ exome

AF:

0.210

Gnomad4 EAS exome

AF:

0.280

Gnomad4 SAS exome

AF:

0.353

Gnomad4 FIN exome

AF:

0.304

Gnomad4 NFE exome

AF:

0.279

Gnomad4 OTH exome

AF:

0.268

GnomAD4 genome

AF:

0.273

AC:

41574

AN:

152240

Hom.:

5786

Cov.:

AF XY:

0.275

AC XY:

20501

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.255

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.218

Gnomad4 EAS

AF:

0.285

Gnomad4 SAS

AF:

0.358

Gnomad4 FIN

AF:

0.307

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.263

Alfa

AF:

0.268

Hom.:

10558

Bravo

AF:

0.274

Asia WGS

AF:

0.290

AC:

1009

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ASRGL1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 04, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over