rs2371767

Positions:

• chr3-64732582-G-C

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+47244G>C 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 0.377 in 151,728 control chromosomes in the GnomAD database, including 12,562 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 0.38 (12562 hom., cov: 30)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+47244G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1	n.404+47244G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57121 AN: 151608 Hom.: 12533 Cov.: 30

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.377 AC: 57194 AN: 151728 Hom.: 12562 Cov.: 30 AF XY: 0.375 AC XY: 27804 AN XY: 74152

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.387

Alfa AF: 0.330 Hom.: 1162

Bravo AF: 0.385

Asia WGS AF: 0.352 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2371767; hg19: chr3-64718258;