rs2218266

Variant names:

• chr3-64922932-G-A
• rs2218266
• ENST00000481312.2:n.653+55675G>A

Variant summary

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

The ENST00000481312.2(ADAMTS9-AS2):​n.653+55675G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,114 control chromosomes in the GnomAD database, including 4,627 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 0.24 (4627 hom., cov: 32)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 0 publications found

Genes affected

ADAMTS9-AS2 (HGNC:42435): (ADAMTS9 antisense RNA 2)

ENSG00000300285 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000481312.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	NR_038264.1		n.897+55675G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	ENST00000481312.2	TSL:1	n.653+55675G>A		intron	N/A
	ADAMTS9-AS2	ENST00000474768.5	TSL:2	n.664-50880G>A		intron	N/A
	ADAMTS9-AS2	ENST00000650103.1		n.832+55675G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36206 AN: 151994 Hom.: 4619 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.238 AC: 36246 AN: 152114 Hom.: 4627 Cov.: 32 AF XY: 0.243 AC XY: 18083 AN XY: 74356

African (AFR) AF: 0.215 AC: 8943 AN: 41516

American (AMR) AF: 0.347 AC: 5295 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1658 AN: 5168

South Asian (SAS) AF: 0.268 AC: 1290 AN: 4820

European-Finnish (FIN) AF: 0.260 AC: 2745 AN: 10572

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14461 AN: 67972

Other (OTH) AF: 0.261 AC: 552 AN: 2114

Alfa AF: 0.229 Hom.: 495

Bravo AF: 0.244

Asia WGS AF: 0.337 AC: 1171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs2218266; hg19: chr3-64908607;