rs2371767

Variant names:

• chr3-64732582-G-C
• rs2371767
• ENST00000460833.2:n.460+47244G>C

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+47244G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,728 control chromosomes in the GnomAD database, including 12,562 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 0.38 (12562 hom., cov: 30)
• Consequence: ADAMTS9-AS2 ENST00000460833.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 42 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+47244G>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000460833.2	n.460+47244G>C		intron_variant	Intron 1 of 1	1
ADAMTS9-AS2	ENST00000481312.2	n.225+47244G>C		intron_variant	Intron 1 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.235+47244G>C		intron_variant	Intron 1 of 4	2

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57121 AN: 151608 Hom.: 12533 Cov.: 30

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.377 AC: 57194 AN: 151728 Hom.: 12562 Cov.: 30 AF XY: 0.375 AC XY: 27804 AN XY: 74152

African (AFR) AF: 0.594 AC: 24549 AN: 41336

American (AMR) AF: 0.271 AC: 4124 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1872 AN: 3458

East Asian (EAS) AF: 0.202 AC: 1036 AN: 5140

South Asian (SAS) AF: 0.516 AC: 2482 AN: 4810

European-Finnish (FIN) AF: 0.224 AC: 2353 AN: 10524

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19460 AN: 67908

Other (OTH) AF: 0.387 AC: 814 AN: 2106

Alfa AF: 0.330 Hom.: 1162

Bravo AF: 0.385

Asia WGS AF: 0.352 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.79
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2371767; hg19: chr3-64718258;