rs7604984

Variant names:

• chr2-215352916-G-A
• rs7604984
• XM_047444489.1:c.1787+835G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-215352916-G-A
• chr2-215352916-G-C

Variant summary

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

The XR_007075418.1(ATIC):​n.1871+835G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,004 control chromosomes in the GnomAD database, including 26,552 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 0.59 (26552 hom., cov: 32)
• Consequence: ATIC XR_007075418.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 15 publications found

Genes affected

ATIC (HGNC:794): (5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase) This gene encodes a bifunctional protein that catalyzes the last two steps of the de novo purine biosynthetic pathway. The N-terminal domain has phosphoribosylaminoimidazolecarboxamide formyltransferase activity, and the C-terminal domain has IMP cyclohydrolase activity. A mutation in this gene results in AICA-ribosiduria. [provided by RefSeq, Sep 2009]

ATIC Gene-Disease associations (from GenCC):

• AICA-ribosiduria

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89583 AN: 151886 Hom.: 26547 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.590 AC: 89622 AN: 152004 Hom.: 26552 Cov.: 32 AF XY: 0.588 AC XY: 43714 AN XY: 74286

African (AFR) AF: 0.563 AC: 23303 AN: 41416

American (AMR) AF: 0.604 AC: 9221 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1704 AN: 3472

East Asian (EAS) AF: 0.719 AC: 3707 AN: 5154

South Asian (SAS) AF: 0.464 AC: 2237 AN: 4818

European-Finnish (FIN) AF: 0.609 AC: 6430 AN: 10550

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41093 AN: 68002

Other (OTH) AF: 0.589 AC: 1243 AN: 2110

Alfa AF: 0.591 Hom.: 85021

Bravo AF: 0.587

Asia WGS AF: 0.552 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.025
DANN	Benign	0.74
PhyloP100		-0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7604984;

hg19: chr2-216217639;