3-64900435-A-G

Variant names:

• chr3-64900435-A-G
• rs1036797
• ENST00000481312.2:n.653+33178A>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+33178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,214 control chromosomes in the GnomAD database, including 43,853 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 0.75 (43853 hom., cov: 33)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	NR_038264.1		n.897+33178A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	ENST00000481312.2	TSL:1	n.653+33178A>G		intron	N/A
	ADAMTS9-AS2	ENST00000474768.5	TSL:2	n.663+33178A>G		intron	N/A
	ADAMTS9-AS2	ENST00000650103.1		n.832+33178A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114708 AN: 152096 Hom.: 43803 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.754 AC: 114819 AN: 152214 Hom.: 43853 Cov.: 33 AF XY: 0.750 AC XY: 55799 AN XY: 74428

African (AFR) AF: 0.851 AC: 35360 AN: 41544

American (AMR) AF: 0.784 AC: 11993 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.718 AC: 2491 AN: 3468

East Asian (EAS) AF: 0.852 AC: 4397 AN: 5160

South Asian (SAS) AF: 0.669 AC: 3231 AN: 4826

European-Finnish (FIN) AF: 0.615 AC: 6513 AN: 10590

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48367 AN: 68016

Other (OTH) AF: 0.745 AC: 1575 AN: 2114

Alfa AF: 0.729 Hom.: 172490

Bravo AF: 0.777

Asia WGS AF: 0.734 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.54
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1036797; hg19: chr3-64886110;