2-189661607-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001353493.2(ASDURF):​c.87C>T​(p.Ser29Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00795 in 399,366 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0068 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0087 ( 19 hom. )

Consequence

ASDURF
NM_001353493.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.231
Variant links:
Genes affected
ASDURF (HGNC:53619): (ASNSD1 upstream open reading frame) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
ASNSD1 (HGNC:24910): (asparagine synthetase domain containing 1) Predicted to enable asparagine synthase (glutamine-hydrolyzing) activity. Predicted to be involved in asparagine biosynthetic process and glutamine metabolic process. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 2-189661607-C-T is Benign according to our data. Variant chr2-189661607-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651759.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.231 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ASDURFNM_001353493.2 linkc.87C>T p.Ser29Ser synonymous_variant Exon 1 of 4 ENST00000607829.6 NP_001340422.1
ASNSD1NM_019048.4 linkc.-226C>T 5_prime_UTR_variant Exon 1 of 6 ENST00000260952.9 NP_061921.2 Q9NWL6-1
ASDURFNM_001353494.2 linkc.87C>T p.Ser29Ser synonymous_variant Exon 1 of 4 NP_001340423.1
ASNSD1NM_001353497.2 linkc.-172C>T 5_prime_UTR_variant Exon 1 of 5 NP_001340426.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ASDURFENST00000607829.6 linkc.87C>T p.Ser29Ser synonymous_variant Exon 1 of 4 2 NM_001353493.2 ENSP00000475224.1 L0R819-1
ENSG00000286165ENST00000606910.5 linkc.87C>T p.Ser29Ser synonymous_variant Exon 1 of 5 3 ENSP00000476091.1 U3KQP1
ASNSD1ENST00000260952 linkc.-226C>T 5_prime_UTR_variant Exon 1 of 6 1 NM_019048.4 ENSP00000260952.4 Q9NWL6-1

Frequencies

GnomAD3 genomes
AF:
0.00681
AC:
1037
AN:
152198
Hom.:
6
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00150
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00288
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.0249
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.00956
Gnomad OTH
AF:
0.00573
GnomAD3 exomes
AF:
0.00850
AC:
73
AN:
8584
Hom.:
0
AF XY:
0.00985
AC XY:
40
AN XY:
4062
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad NFE exome
AF:
0.00954
Gnomad OTH exome
AF:
0.00595
GnomAD4 exome
AF:
0.00865
AC:
2137
AN:
247050
Hom.:
19
Cov.:
0
AF XY:
0.00848
AC XY:
1062
AN XY:
125296
show subpopulations
Gnomad4 AFR exome
AF:
0.00139
Gnomad4 AMR exome
AF:
0.00323
Gnomad4 ASJ exome
AF:
0.000974
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000329
Gnomad4 FIN exome
AF:
0.0248
Gnomad4 NFE exome
AF:
0.00924
Gnomad4 OTH exome
AF:
0.00622
GnomAD4 genome
AF:
0.00681
AC:
1037
AN:
152316
Hom.:
6
Cov.:
32
AF XY:
0.00690
AC XY:
514
AN XY:
74478
show subpopulations
Gnomad4 AFR
AF:
0.00149
Gnomad4 AMR
AF:
0.00288
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.0249
Gnomad4 NFE
AF:
0.00956
Gnomad4 OTH
AF:
0.00567
Alfa
AF:
0.00762
Hom.:
2
Bravo
AF:
0.00523
Asia WGS
AF:
0.00115
AC:
4
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

ASDURF: BP4, BP7, BS2; ASNSD1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
10
DANN
Benign
0.83

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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.

Other links and lift over

dbSNP: rs187165993; hg19: chr2-190526333; API