rs1523448

Variant names:

• chr3-64846717-C-A
• rs1523448
• ENST00000481312.2:n.564-20451C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-64846717-C-A
• chr3-64846717-C-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.564-20451C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,106 control chromosomes in the GnomAD database, including 58,741 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 0.88 (58741 hom., cov: 31)
• Consequence: ADAMTS9-AS2 ENST00000481312.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000481312.2. 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.808-20451C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAMTS9-AS2	ENST00000481312.2	TSL:1	n.564-20451C>A		intron	N/A
	ADAMTS9-AS2	ENST00000474768.5	TSL:2	n.574-20451C>A		intron	N/A
	ADAMTS9-AS2	ENST00000650103.1		n.743-20451C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133235 AN: 151988 Hom.: 58698 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.877 AC: 133336 AN: 152106 Hom.: 58741 Cov.: 31 AF XY: 0.876 AC XY: 65121 AN XY: 74348

African (AFR) AF: 0.785 AC: 32557 AN: 41460

American (AMR) AF: 0.901 AC: 13749 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3207 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4416 AN: 5146

South Asian (SAS) AF: 0.798 AC: 3851 AN: 4826

European-Finnish (FIN) AF: 0.944 AC: 10013 AN: 10606

Middle Eastern (MID) AF: 0.918 AC: 268 AN: 292

European-Non Finnish (NFE) AF: 0.919 AC: 62483 AN: 68020

Other (OTH) AF: 0.893 AC: 1885 AN: 2112

Alfa AF: 0.906 Hom.: 29807

Bravo AF: 0.871

Asia WGS AF: 0.845 AC: 2941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.91
DANN	Benign	0.20
PhyloP100		0.36

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: rs1523448;

hg19: chr3-64832392;