rs3008633

chr1-222671498-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
AIDA	NM_022831.4	c.707-1248A>G		intron_variant		ENST00000340020.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AIDA	ENST00000340020.11	c.707-1248A>G		intron_variant		1	NM_022831.4	P1

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

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.809

Alfa AF: 0.802 Hom.: 7366

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

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: rs3008633; hg19: chr1-222844840;