rs1523448

chr3-64846717-C-Achr3-64846717-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038264.1(ADAMTS9-AS2):n.808-20451C>A variant causes a intron, non coding transcript 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 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS9-AS2	NR_038264.1	n.808-20451C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1	n.743-20451C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.919

Gnomad4 OTH AF: 0.893

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.91
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1523448; hg19: chr3-64832392;