rs3008633

Variant names:

• chr1-222671498-T-C
• rs3008633
• NM_022831.4:c.707-1248A>G

Variant summary

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

The NM_022831.4(AIDA):​c.707-1248A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,082 control chromosomes in the GnomAD database, including 48,089 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 0.77 (48089 hom., cov: 31)
• Consequence: AIDA NM_022831.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 6 publications found

Genes affected

AIDA (HGNC:25761): (axin interactor, dorsalization associated) Predicted to enable phosphatidylinositol binding activity. Acts upstream of or within negative regulation of JUN kinase activity. Predicted to be located in cytoplasm. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AIDA	NM_022831.4	c.707-1248A>G		intron_variant	Intron 8 of 9	ENST00000340020.11	NP_073742.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AIDA	ENST00000340020.11	c.707-1248A>G		intron_variant	Intron 8 of 9	1	NM_022831.4	ENSP00000339161.6

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117147 AN: 151964 Hom.: 48078 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.771 AC: 117181 AN: 152082 Hom.: 48089 Cov.: 31 AF XY: 0.775 AC XY: 57638 AN XY: 74364

African (AFR) AF: 0.454 AC: 18798 AN: 41382

American (AMR) AF: 0.889 AC: 13592 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3083 AN: 3472

East Asian (EAS) AF: 0.852 AC: 4409 AN: 5172

South Asian (SAS) AF: 0.847 AC: 4090 AN: 4828

European-Finnish (FIN) AF: 0.921 AC: 9766 AN: 10606

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60603 AN: 68012

Other (OTH) AF: 0.809 AC: 1709 AN: 2112

Alfa AF: 0.818 Hom.: 16296

Bravo AF: 0.755

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.71
PhyloP100		-0.20
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: rs3008633; hg19: chr1-222844840;