rs3102460

Positions:

• chr1-244413415-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ADSS2	NM_001126.5	c.1169-1979G>A		intron_variant		ENST00000366535.4	NP_001117.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADSS2	ENST00000366535.4	c.1169-1979G>A		intron_variant		1	NM_001126.5	ENSP00000355493	P1
ADSS2	ENST00000468215.1	n.738-1979G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.713

Alfa AF: 0.743 Hom.: 72134

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

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

Other links and lift over

dbSNP: rs3102460; hg19: chr1-244576717;