rs2371765

Variant names:

• chr3-64750901-G-A
• rs2371765
• ENST00000460833.2:n.461-48564G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-64750901-G-A
• chr3-64750901-G-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.461-48564G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,900 control chromosomes in the GnomAD database, including 16,473 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 0.45 (16473 hom., cov: 32)
• Consequence: ADAMTS9-AS2 ENST00000460833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 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.470-48564G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	ENST00000460833.2	TSL:1	n.461-48564G>A		intron	N/A
	ADAMTS9-AS2	ENST00000481312.2	TSL:1	n.226-48564G>A		intron	N/A
	ADAMTS9-AS2	ENST00000474768.5	TSL:2	n.236-48564G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68929 AN: 151782 Hom.: 16452 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.454 AC: 68986 AN: 151900 Hom.: 16473 Cov.: 32 AF XY: 0.460 AC XY: 34114 AN XY: 74194

African (AFR) AF: 0.354 AC: 14653 AN: 41438

American (AMR) AF: 0.580 AC: 8860 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3466

East Asian (EAS) AF: 0.725 AC: 3722 AN: 5134

South Asian (SAS) AF: 0.433 AC: 2086 AN: 4820

European-Finnish (FIN) AF: 0.525 AC: 5526 AN: 10526

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31434 AN: 67934

Other (OTH) AF: 0.450 AC: 950 AN: 2112

Alfa AF: 0.471 Hom.: 6699

Bravo AF: 0.455

Asia WGS AF: 0.614 AC: 2133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.54
DANN	Benign	0.83
PhyloP100		-0.71

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2371765;

hg19: chr3-64736577;