3-64921609-A-G

Variant names:

• chr3-64921609-A-G
• rs2280585
• ENST00000481312.2:n.653+54352A>G

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+54352A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,008 control chromosomes in the GnomAD database, including 10,570 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 0.35 (10570 hom., cov: 32)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.897+54352A>G		intron_variant	Intron 4 of 5
LOC105377124	XR_001740437.2	n.262+20895T>C		intron_variant	Intron 2 of 3
LOC105377124	XR_007095946.1	n.262+20895T>C		intron_variant	Intron 2 of 3
LOC105377124	XR_007095948.1	n.262+20895T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000481312.2	n.653+54352A>G		intron_variant	Intron 4 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.664-52203A>G		intron_variant	Intron 4 of 4	2
ADAMTS9-AS2	ENST00000650103.1	n.832+54352A>G		intron_variant	Intron 4 of 11

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53168 AN: 151890 Hom.: 10557 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.350 AC: 53232 AN: 152008 Hom.: 10570 Cov.: 32 AF XY: 0.359 AC XY: 26640 AN XY: 74290

African (AFR) AF: 0.477 AC: 19759 AN: 41418

American (AMR) AF: 0.464 AC: 7077 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3468

East Asian (EAS) AF: 0.584 AC: 3017 AN: 5166

South Asian (SAS) AF: 0.357 AC: 1718 AN: 4818

European-Finnish (FIN) AF: 0.334 AC: 3525 AN: 10560

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15922 AN: 67994

Other (OTH) AF: 0.359 AC: 758 AN: 2112

Alfa AF: 0.284 Hom.: 19293

Bravo AF: 0.370

Asia WGS AF: 0.479 AC: 1667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.39
DANN	Benign	0.35
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2280585; hg19: chr3-64907284;