rs4411878

Variant names:

• chr3-64717989-C-T
• rs4411878
• ENST00000460833.2:n.460+32651C>T

Variant summary

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

The ENST00000460833.2(ADAMTS9-AS2):​n.460+32651C>T 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 152,082 control chromosomes in the GnomAD database, including 4,653 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 (4653 hom., cov: 32)
• Consequence: ADAMTS9-AS2 ENST00000460833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 22 publications found

Genes affected

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

ENSG00000300305 (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 (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460833.2. 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.469+32651C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	ENST00000460833.2	TSL:1	n.460+32651C>T		intron	N/A
	ADAMTS9-AS2	ENST00000481312.2	TSL:1	n.225+32651C>T		intron	N/A
	ADAMTS9-AS2	ENST00000474768.5	TSL:2	n.235+32651C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36129 AN: 151962 Hom.: 4649 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.238 AC: 36140 AN: 152082 Hom.: 4653 Cov.: 32 AF XY: 0.238 AC XY: 17662 AN XY: 74348

African (AFR) AF: 0.206 AC: 8546 AN: 41488

American (AMR) AF: 0.202 AC: 3082 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1047 AN: 5148

South Asian (SAS) AF: 0.472 AC: 2274 AN: 4814

European-Finnish (FIN) AF: 0.194 AC: 2052 AN: 10592

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16599 AN: 67976

Other (OTH) AF: 0.267 AC: 564 AN: 2112

Alfa AF: 0.252 Hom.: 16347

Bravo AF: 0.231

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.32
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4411878; hg19: chr3-64703665;