3-64900435-A-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.897+33178A>G 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 0.754 in 152,214 control chromosomes in the GnomAD database, including 43,853 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 0.75 (43853 hom., cov: 33)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

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

LOC105377124 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADAMTS9-AS2	NR_038264.1	n.897+33178A>G		intron_variant, non_coding_transcript_variant
LOC105377124	XR_007095948.1	n.263-23962T>C		intron_variant, non_coding_transcript_variant
LOC105377124	XR_001740437.2	n.263-5788T>C		intron_variant, non_coding_transcript_variant
LOC105377124	XR_007095946.1	n.263-5788T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADAMTS9-AS2	ENST00000650103.1	n.832+33178A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114708 AN: 152096 Hom.: 43803 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.754 AC: 114819 AN: 152214 Hom.: 43853 Cov.: 33 AF XY: 0.750 AC XY: 55799 AN XY: 74428

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.745

Alfa AF: 0.722 Hom.: 79807

Bravo AF: 0.777

Asia WGS AF: 0.734 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.54
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1036797; hg19: chr3-64886110;