rs3102460

Variant names:

• chr1-244413415-C-T
• rs3102460
• NM_001126.5:c.1169-1979G>A

Variant summary

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

The NM_001126.5(ADSS2):​c.1169-1979G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 152,018 control chromosomes in the GnomAD database, including 39,963 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 0.72 (39963 hom., cov: 31)
• Consequence: ADSS2 NM_001126.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADSS2	NM_001126.5	c.1169-1979G>A		intron_variant	Intron 11 of 12	ENST00000366535.4	NP_001117.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADSS2	ENST00000366535.4	c.1169-1979G>A		intron_variant	Intron 11 of 12	1	NM_001126.5	ENSP00000355493.3
ADSS2	ENST00000468215.1	n.738-1979G>A		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109933 AN: 151900 Hom.: 39955 Cov.: 31

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.723 AC: 109982 AN: 152018 Hom.: 39963 Cov.: 31 AF XY: 0.721 AC XY: 53582 AN XY: 74324

African (AFR) AF: 0.675 AC: 27969 AN: 41422

American (AMR) AF: 0.700 AC: 10692 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2517 AN: 3470

East Asian (EAS) AF: 0.701 AC: 3620 AN: 5166

South Asian (SAS) AF: 0.727 AC: 3499 AN: 4814

European-Finnish (FIN) AF: 0.749 AC: 7910 AN: 10564

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51275 AN: 67988

Other (OTH) AF: 0.713 AC: 1504 AN: 2110

Alfa AF: 0.740 Hom.: 167738

Bravo AF: 0.718

Asia WGS AF: 0.681 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.40
PhyloP100		-0.036
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: rs3102460; hg19: chr1-244576717;