chr1-244440440-C-A

Variant names:

• chr1-244440440-C-A
• rs3006001
• NM_001126.5:c.184-2672G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001126.5(ADSS2):​c.184-2672G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 152,114 control chromosomes in the GnomAD database, including 54,907 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 (54907 hom., cov: 32)
• Consequence: ADSS2 NM_001126.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADSS2	NM_001126.5	c.184-2672G>T		intron_variant	Intron 1 of 12	ENST00000366535.4	NP_001117.2
ADSS2	NM_001365073.2	c.184-2672G>T		intron_variant	Intron 1 of 12		NP_001352002.1
ADSS2	XM_047447581.1	c.4-2672G>T		intron_variant	Intron 2 of 13		XP_047303537.1
ADSS2	XM_047447585.1	c.4-2672G>T		intron_variant	Intron 1 of 12		XP_047303541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADSS2	ENST00000366535.4	c.184-2672G>T		intron_variant	Intron 1 of 12	1	NM_001126.5	ENSP00000355493.3

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128634 AN: 151996 Hom.: 54859 Cov.: 32

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.917

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.854

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.846 AC: 128737 AN: 152114 Hom.: 54907 Cov.: 32 AF XY: 0.838 AC XY: 62311 AN XY: 74336

African (AFR) AF: 0.932 AC: 38710 AN: 41524

American (AMR) AF: 0.859 AC: 13129 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2884 AN: 3466

East Asian (EAS) AF: 0.783 AC: 4036 AN: 5156

South Asian (SAS) AF: 0.670 AC: 3227 AN: 4816

European-Finnish (FIN) AF: 0.725 AC: 7646 AN: 10552

Middle Eastern (MID) AF: 0.908 AC: 265 AN: 292

European-Non Finnish (NFE) AF: 0.828 AC: 56322 AN: 68006

Other (OTH) AF: 0.853 AC: 1799 AN: 2110

Alfa AF: 0.783 Hom.: 2345

Bravo AF: 0.863

Asia WGS AF: 0.771 AC: 2682 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.34
PhyloP100		0.032
Mutation Taster		=100/0	polymorphism (auto)

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: rs3006001; hg19: chr1-244603742;