3-64921609-A-G

Position:

• chr3-64921609-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+54352A>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 0.35 in 152,008 control chromosomes in the GnomAD database, including 10,570 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 0.35 (10570 hom., cov: 32)
• Consequence: ADAMTS9-AS2 NR_038264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAMTS9-AS2	NR_038264.1	n.897+54352A>G		intron_variant, non_coding_transcript_variant
LOC105377124	XR_007095948.1	n.262+20895T>C		intron_variant, non_coding_transcript_variant
LOC105377124	XR_001740437.2	n.262+20895T>C		intron_variant, non_coding_transcript_variant
LOC105377124	XR_007095946.1	n.262+20895T>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.832+54352A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53168 AN: 151890 Hom.: 10557 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.350 AC: 53232 AN: 152008 Hom.: 10570 Cov.: 32 AF XY: 0.359 AC XY: 26640 AN XY: 74290

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.359

Alfa AF: 0.267 Hom.: 10087

Bravo AF: 0.370

Asia WGS AF: 0.479 AC: 1667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.39
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2280585; hg19: chr3-64907284;