rs812651

Variant names:

• chr3-64932947-G-A
• rs812651
• ENST00000481312.2:n.653+65690G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-64932947-G-A
• chr3-64932947-G-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000481312.2(ADAMTS9-AS2):​n.653+65690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000329 in 151,852 control chromosomes in the GnomAD database, including 1 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 0.00033 (1 hom., cov: 30)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 2 publications found

Genes affected

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

ENSG00000300285 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.897+65690G>A		intron_variant	Intron 4 of 5
LOC105377124	XR_001740437.2	n.262+9557C>T		intron_variant	Intron 2 of 3
LOC105377124	XR_007095946.1	n.262+9557C>T		intron_variant	Intron 2 of 3
LOC105377124	XR_007095948.1	n.262+9557C>T		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+65690G>A		intron_variant	Intron 4 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.664-40865G>A		intron_variant	Intron 4 of 4	2
ADAMTS9-AS2	ENST00000650103.1	n.832+65690G>A		intron_variant	Intron 4 of 11

Frequencies

GnomAD3 genomes AF: 0.000330 AC: 50 AN: 151734 Hom.: 1 Cov.: 30

Gnomad AFR AF: 0.0000485

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00318

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00311

Gnomad FIN AF: 0.000285

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000329 AC: 50 AN: 151852 Hom.: 1 Cov.: 30 AF XY: 0.000431 AC XY: 32 AN XY: 74182

African (AFR) AF: 0.0000483 AC: 2 AN: 41382

American (AMR) AF: 0.000196 AC: 3 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00318 AC: 11 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5122

South Asian (SAS) AF: 0.00311 AC: 15 AN: 4816

European-Finnish (FIN) AF: 0.000285 AC: 3 AN: 10522

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000235 AC: 16 AN: 67968

Other (OTH) AF: 0.00 AC: 0 AN: 2104

Alfa AF: 0.000123 Hom.: 1722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.90
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs812651; hg19: chr3-64918622;