rs7433808

chr3-64741410-A-T

Variant summary

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

The NR_038264.1(ADAMTS9-AS2):n.469+56072A>T 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 0.291 in 152,078 control chromosomes in the GnomAD database, including 7,082 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 0.29 (7079 hom., cov: 32)
  • Exomes 𝑓: 0.28 (3 hom.)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+56072A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1	n.404+56072A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44222 AN: 151914 Hom.: 7070 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.314

GnomAD4 exome AF: 0.283 AC: 13 AN: 46 Hom.: 3 AF XY: 0.333 AC XY: 12 AN XY: 36

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.206

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.291 AC: 44258 AN: 152032 Hom.: 7079 Cov.: 32 AF XY: 0.289 AC XY: 21475 AN XY: 74274

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.313

Alfa AF: 0.257 Hom.: 699

Bravo AF: 0.293

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.4
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7433808; hg19: chr3-64727086;