rs2371765

Positions:

• chr3-64750901-G-A
• chr3-64750901-G-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.470-48564G>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 0.454 in 151,900 control chromosomes in the GnomAD database, including 16,473 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 0.45 (16473 hom., cov: 32)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

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 (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.470-48564G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1	n.405-48564G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68929 AN: 151782 Hom.: 16452 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.454 AC: 68986 AN: 151900 Hom.: 16473 Cov.: 32 AF XY: 0.460 AC XY: 34114 AN XY: 74194

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.450

Alfa AF: 0.476 Hom.: 4374

Bravo AF: 0.455

Asia WGS AF: 0.614 AC: 2133 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	0.54
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2371765; hg19: chr3-64736577;