1-244423764-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000366535.4(ADSS2):​c.581+189T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,026 control chromosomes in the GnomAD database, including 16,044 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 0.45 ( 16044 hom., cov: 32)

Consequence

ADSS2
ENST00000366535.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.596
Variant links:
Genes affected
ADSS2 (HGNC:292): (adenylosuccinate synthase 2) This gene encodes the enzyme adenylosuccinate synthetase which catalyzes the first committed step in the conversion of inosine monophosphate to adenosine monophosphate. A pseudogene of this gene is found on chromosome 17.[provided by RefSeq, Nov 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADSS2NM_001126.5 linkuse as main transcriptc.581+189T>A intron_variant ENST00000366535.4 NP_001117.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADSS2ENST00000366535.4 linkuse as main transcriptc.581+189T>A intron_variant 1 NM_001126.5 ENSP00000355493 P1
ADSS2ENST00000462358.1 linkuse as main transcriptn.702+189T>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.453
AC:
68748
AN:
151908
Hom.:
16007
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.512
Gnomad AMI
AF:
0.310
Gnomad AMR
AF:
0.426
Gnomad ASJ
AF:
0.409
Gnomad EAS
AF:
0.728
Gnomad SAS
AF:
0.377
Gnomad FIN
AF:
0.441
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.412
Gnomad OTH
AF:
0.448
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.453
AC:
68829
AN:
152026
Hom.:
16044
Cov.:
32
AF XY:
0.455
AC XY:
33787
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.513
Gnomad4 AMR
AF:
0.426
Gnomad4 ASJ
AF:
0.409
Gnomad4 EAS
AF:
0.728
Gnomad4 SAS
AF:
0.376
Gnomad4 FIN
AF:
0.441
Gnomad4 NFE
AF:
0.412
Gnomad4 OTH
AF:
0.451
Alfa
AF:
0.437
Hom.:
1847
Bravo
AF:
0.459
Asia WGS
AF:
0.568
AC:
1974
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
6.5
DANN
Benign
0.75

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

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

Other links and lift over

dbSNP: rs3127459; hg19: chr1-244587066; API