3-64849152-T-G

Variant names:

• chr3-64849152-T-G
• rs877523
• ENST00000481312.2:n.564-18016T>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.564-18016T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,866 control chromosomes in the GnomAD database, including 18,762 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 0.49 (18762 hom., cov: 31)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.808-18016T>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000481312.2	n.564-18016T>G		intron_variant	Intron 3 of 5	1
ADAMTS9-AS2	ENST00000474768.5	n.574-18016T>G		intron_variant	Intron 3 of 4	2
ADAMTS9-AS2	ENST00000650103.1	n.743-18016T>G		intron_variant	Intron 3 of 11

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74706 AN: 151748 Hom.: 18730 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.493 AC: 74798 AN: 151866 Hom.: 18762 Cov.: 31 AF XY: 0.496 AC XY: 36837 AN XY: 74216

African (AFR) AF: 0.494 AC: 20433 AN: 41398

American (AMR) AF: 0.565 AC: 8628 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2071 AN: 3470

East Asian (EAS) AF: 0.787 AC: 4055 AN: 5154

South Asian (SAS) AF: 0.475 AC: 2279 AN: 4800

European-Finnish (FIN) AF: 0.474 AC: 4995 AN: 10536

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30642 AN: 67928

Other (OTH) AF: 0.513 AC: 1083 AN: 2112

Alfa AF: 0.469 Hom.: 44212

Bravo AF: 0.501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.30
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs877523; hg19: chr3-64834827;