3-64695029-C-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+9691C>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 0.497 in 151,258 control chromosomes in the GnomAD database, including 19,476 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 0.50 (19476 hom., cov: 29)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

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 (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS9-AS2	NR_038264.1	n.469+9691C>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+9691C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75134 AN: 151144 Hom.: 19456 Cov.: 29

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.497 AC: 75200 AN: 151258 Hom.: 19476 Cov.: 29 AF XY: 0.507 AC XY: 37470 AN XY: 73876

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.527

Alfa AF: 0.475 Hom.: 6711

Bravo AF: 0.497

Asia WGS AF: 0.797 AC: 2768 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.6
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4521216; hg19: chr3-64680705;